Bartender_2024_itps.tar.gz

ITPS/0000755174611600001440000000000014601235002011176 5ustar  gperei01usersITPS/PET/0000755174611600001440000000000014601235110011626 5ustar  gperei01usersITPS/PET/PyCGTool/0000755174611600001440000000000014601243474013302 5ustar  gperei01usersITPS/PET/PyCGTool/PET.itp0000750174611600001440000000371014601237234014444 0ustar  gperei01users[ moleculetype ]
; molname    nrexcl
  PET         1

 [ atoms ]
; nr type resnr residue atom cgnr charge mass  
   1  SQ5n    0    PET    B1     1    -1     
   2  TC5     0    PET    B2     2     0 
   3  TC5     0    PET    B3     3     0
   4  TC5     0    PET    B4     4     0   
   5  N4a     0    PET    B5     5     0   
   6  N4a     0    PET    B6     6     0
   7  TC5     0    PET    B7     7     0
   8  TC5     0    PET    B8     8     0
   9  TC5     0    PET    B9     9     0
   10 N4a     0    PET    B10    10    0
   11 TP1     0    PET    B11    11    0
   
[bonds]
; i j  funct    length   force.c.
  3 5   1      0.38	4335.40
  5 6   1      0.29	3264.19
  6 7   1      0.37	4419.52
 10 11  1      0.27	4822.71

  
[constraints]
; i j  funct    length  
  1 2   1      0.22     
  2 3   1      0.23     
  2 4   1      0.23     
  3 4   1      0.27    
  7 8   1      0.27     
  7 9   1      0.23     
  8 9   1      0.23     
  9 10  1      0.31     
   

[ angles ] 
; i   j   k   funct   ref.angle   force_k
  1     2       3          1     144.96   1500    ; adjusted      - 5000 kf is fucking insane.
  4     3       5          1     68.80	   103.04 
  3     5       6          1     112.62    38.70 
  5     6       7          1     109.39    37.13
  6     7       8          1     71.32	   101.21 
  7     9       10         1     146.68    206.34 
  9     10      11         1     122.68    164.64 
  4     6       7          1     80.78     30 
  1     6       11         1     70.34     30


[ dihedrals ]
; i j k l   funct  ref.angle force_k
  7     9       10   11         1      -0.43 0.87   3
   
  3     5       6    7          2      0.09	3.36  
  2     3       4    1          2      0.00	1288.35   
  2     4       3    5          2     179.99	220.33
  7     8       9    6          2      0.02	176.22
  9     7       8    10         2      0.01	502.59 

  
[ exclusions ] 
;ring1

1 2 3 4
2 3 4 
3 4 
 
4 5
5 6
6 7
6 8

;ring2

7 8 9 10
8 9 10
9 10
ITPS/PET/PyCGTool/PET_CG.gro0000750174611600001440000000102414601243474015007 0ustar  gperei01usersGenerated with cgbuilder
11
    1PET     B1    1   0.211   0.016  -0.019
    1PET     B2    2   0.001  -0.051   0.029
    1PET     B3    3  -0.199   0.002   0.032
    1PET     B4    4  -0.122  -0.202   0.100
    1PET     B5    5  -0.391  -0.222   0.233
    1PET     B6    6  -0.403  -0.521   0.430
    1PET     B7    7  -0.373  -0.461   0.786
    1PET     B8    8  -0.402  -0.688   0.790
    1PET     B9    9  -0.377  -0.572   0.961
    1PET    B10   10  -0.363  -0.624   1.280
    1PET    B11   11  -0.383  -0.890   1.445
10 10 10
ITPS/PET/Bartender/0000755174611600001440000000000014601243444013545 5ustar  gperei01usersITPS/PET/Bartender/PET_CG.gro0000750174611600001440000000102414601243444015252 0ustar  gperei01usersGenerated with cgbuilder
11
    1PET     B1    1   0.211   0.016  -0.019
    1PET     B2    2   0.001  -0.051   0.029
    1PET     B3    3  -0.199   0.002   0.032
    1PET     B4    4  -0.122  -0.202   0.100
    1PET     B5    5  -0.391  -0.222   0.233
    1PET     B6    6  -0.403  -0.521   0.430
    1PET     B7    7  -0.373  -0.461   0.786
    1PET     B8    8  -0.402  -0.688   0.790
    1PET     B9    9  -0.377  -0.572   0.961
    1PET    B10   10  -0.363  -0.624   1.280
    1PET    B11   11  -0.383  -0.890   1.445
10 10 10
ITPS/PET/Bartender/PET.itp0000750174611600001440000000427014601237176014721 0ustar  gperei01users[ moleculetype ]
; molname    nrexcl
  PET         1

 [ atoms ]
; nr type resnr residue atom cgnr charge mass  
   1  SQ5n    0    PET    B1     1    -1     
   2  TC5     0    PET    B2     2     0 
   3  TC5     0    PET    B3     3     0
   4  TC5     0    PET    B4     4     0   
   5  N4a     0    PET    B5     5     0   
   6  N4a     0    PET    B6     6     0
   7  TC5     0    PET    B7     7     0
   8  TC5     0    PET    B8     8     0
   9  TC5     0    PET    B9     9     0
   10 N4a     0    PET    B10    10    0
   11 TP1     0    PET    B11    11    0
   
[bonds]
; i j  funct    length   force.c.
  3 5   1      0.375     21532.69 ; rmsd:     1.25
  5 6   1      0.316     11843.24 ; rmsd:     0.77
  6 7   1      0.375     21503.17 ; rmsd:     1.42
 10 11  1      0.267      6028.95 ; rmsd:     1.49
  
[constraints]
; i j  funct    length  
  1 2   1      0.217     
  2 3   1      0.233     
  2 4   1      0.233     
  3 4   1      0.265    
  7 8   1      0.265     
  7 9   1      0.233     
  8 9   1      0.233     
  9 10  1      0.314     
   

[ angles ] 
; i   j   k   funct   ref.angle   force_k
  1     2       3          1     144.92   1698.48 
  4     3       5          1     69.97    244.11 
  3     5       6          1     112.65   44.31 
  5     6       7          1     112.00   45.76 
  6     7       8          1     70.23    253.77 
  7     9       10         1     145.61   154.55 
  9     10      11         1     124.12   123.25 
  4     6       7          1     84.80    30 ; increased value, was too low
  1     6       11         1     75.64    30 ; increased value, was too low


[ dihedrals ]
; i j k l   funct  ref.angle force_k
  7     9       10   11         3      1.03 -0.65  8.23 -3.41 -9.23  3.93
  
  3     5       6    7          2      0.00      3.37 ; rmsd:     2.01   
  2     3       4    1          2      0.00   1246.94 ; rmsd:     0.22   
  2     4       3    5          2     180.00    225.48 ; rmsd:     0.34   
  7     8       9    6          2      0.00    163.58 ; rmsd:     0.58   
  9     7       8    10         2      0.00    502.16 ; rmsd:     0.37   

  
[ exclusions ] 
;ring1

1 2 3 4
2 3 4 
3 4 
 
4 5
5 6
6 7
6 8

;ring2

7 8 9 10
8 9 10
9 10
ITPS/PET/Human/0000755174611600001440000000000014601243471012707 5ustar  gperei01usersITPS/PET/Human/PET_CG.gro0000750174611600001440000000102414601243472014415 0ustar  gperei01usersGenerated with cgbuilder
11
    1PET     B1    1   0.211   0.016  -0.019
    1PET     B2    2   0.001  -0.051   0.029
    1PET     B3    3  -0.199   0.002   0.032
    1PET     B4    4  -0.122  -0.202   0.100
    1PET     B5    5  -0.391  -0.222   0.233
    1PET     B6    6  -0.403  -0.521   0.430
    1PET     B7    7  -0.373  -0.461   0.786
    1PET     B8    8  -0.402  -0.688   0.790
    1PET     B9    9  -0.377  -0.572   0.961
    1PET    B10   10  -0.363  -0.624   1.280
    1PET    B11   11  -0.383  -0.890   1.445
10 10 10
ITPS/PET/Human/PET.itp0000750174611600001440000000360314601237220014050 0ustar  gperei01users[ moleculetype ]
; molname    nrexcl
  PET         1

 [ atoms ]
; nr type resnr residue atom cgnr charge mass  
   1  SQ5n    0    PET    B1     1    -1     
   2  TC5     0    PET    B2     2     0 
   3  TC5     0    PET    B3     3     0
   4  TC5     0    PET    B4     4     0   
   5  N4a     0    PET    B5     5     0   
   6  N4a     0    PET    B6     6     0
   7  TC5     0    PET    B7     7     0
   8  TC5     0    PET    B8     8     0
   9  TC5     0    PET    B9     9     0
   10 N4a     0    PET    B10    10    0
   11 TP1     0    PET    B11    11    0
   
[bonds]
; i j  funct    length   force.c.
  3 5   1      0.377      7500   
  5 6   1      0.302      7100 
  6 7   1      0.371     10000 
 10 11  1      0.269      5000
  
[constraints]
; i j  funct    length  
  1 2   1      0.217     
  2 3   1      0.233     
  2 4   1      0.233    
  3 4   1      0.265     
  7 8   1      0.265     
  7 9   1      0.233     
  8 9   1      0.233     
  9 10  1      0.314     


[ angles ] 
; i   j   k   funct   ref.angle   force_k
  1     2       3          1     145   1600 
  4     3       5          1      69    400 
  3     5       6          1     113     25 
  5     6       7          1     110     25 
  6     7       8          1      70    250
  7     9       10         1     146    210 
  9     10      11         1     123    110
  4     6        7         1      80    30
  1     6       11         1      70    30

  
[ dihedrals ]
; i j k l   funct  ref.angle force_k
  3     5        6    7         2          0      1
  7     9       10   11         1        180      2   3

  2     3       4    1          2         0    920 
  2     4       3    5          2       180    220    
  7     8       9    6          2         0    180
  9     7       8    10         2         0    400
  
[ exclusions ] 
;ring1

1 2 3 4
2 3 4 
3 4 
 
4 5
5 6
6 7
6 8

;ring2

7 8 9 10
8 9 10
9 10
ITPS/M23/0000755174611600001440000000000014601235110011537 5ustar  gperei01usersITPS/M23/Human/0000755174611600001440000000000014601243141012612 5ustar  gperei01usersITPS/M23/Human/M23.itp0000750174611600001440000000216714601240517013701 0ustar  gperei01users[ moleculetype ]
; molname    nrexcl
  M23         1

 [ atoms ]
; nr type resnr residue atom cgnr charge mass  
   1  SC1    0    M23    B1     1     0     
   2   C4    0    M23    B2     2     0 
   3  TC1    0    M23    B3     3     0
   4  TC5    0    M23    B4     4     0   
   5  SC1    0    M23    B5     5     0   
   6  SC3    0    M23    B6     6     0
   7  SC3    0    M23    B7     7     0
  
[bonds]
; i j  funct    length   force.c.
  1 2   1      0.500      5000 
  2 3   1      0.370      7500 
  3 4   1      0.249     15000 
  4 5   1      0.290      8000
  5 6   1      0.333     10000

  
[constraints]
; i j  funct    length  
  6 7   1      0.250       
 
[angles]
; i     j       k       funct   angle   force_constant
  1     2       3          1     150      25 
  2     3       4          1     140      25 
  3     4       5          1     145     200 
  4     5       6          1     140     400 
  5     6       7          1     100     300   

[ dihedrals ]
;  i j k m       type   phase  kf  mult
    3 4 5 6        2	  0    11    
    4 5 6 7        1     180    2     3


[ exclusions ]
4 5 6 7
5 6 7
6 7

ITPS/M23/Human/M23_CG.gro0000750174611600001440000000054014601243141014232 0ustar  gperei01usersGenerated with cgbuilder
7
    1M23     B1    1   0.004   0.100   0.043
    1M23     B2    2  -0.351   0.051   0.307
    1M23     B3    3  -0.622   0.000   0.545
    1M23     B4    4  -0.835   0.049   0.645
    1M23     B5    5  -1.117   0.167   0.629
    1M23     B6    6  -1.439   0.199   0.338
    1M23     B7    7  -1.334   0.370   0.478
10 10 10

ITPS/M23/Bartender/0000755174611600001440000000000014601243131013447 5ustar  gperei01usersITPS/M23/Bartender/M23.itp0000750174611600001440000000254514601240471014536 0ustar  gperei01users[ moleculetype ]
; molname    nrexcl
  M23         1

 [ atoms ]
; nr type resnr residue atom cgnr charge mass  
   1  SC1    0    M23    B1     1     0     
   2   C4    0    M23    B2     2     0 
   3  TC1    0    M23    B3     3     0
   4  TC5    0    M23    B4     4     0   
   5  SC1    0    M23    B5     5     0   
   6  SC3    0    M23    B6     6     0
   7  SC3    0    M23    B7     7     0
  
[bonds]
; i j  funct    length   force.c.
  1 2   1      0.460      2500      ; adjusted with rule 
  2 3   1      0.347      5906.62 
  3 4   1      0.247     21493.92 
  4 5   1      0.283      9867.19 
  5 6   1      0.316     10426.68 
[constraints]
; i j  funct    length  
  6 7   1      0.241    
  
[angles]
; i     j       k       funct   angle   force_constant
  1     2       3          1     133.19     30.69 
  2     3       4          1     137.20     17.21 
  3     4       5          1    143    200    ; rule that if too close to 150, bump by 10 degrees or more (original was 157), also increased KF so it does not go to 180
  4     5       6          1     126.33     400   ; adjusted kf
  5     6       7          1     130.77     62.30   

[ dihedrals ]
;  i j k m       type   phase  kf  mult
3     4       5    6          2      0.00     17.54 
4     5       6    7          3      1.74 -4.04 -1.66  5.30  0.88 -0.58

[ exclusions ]
4 5 6 7
5 6 7
6 7
ITPS/M23/Bartender/M23_CG.gro0000750174611600001440000000054014601243131015067 0ustar  gperei01usersGenerated with cgbuilder
7
    1M23     B1    1   0.004   0.100   0.043
    1M23     B2    2  -0.351   0.051   0.307
    1M23     B3    3  -0.622   0.000   0.545
    1M23     B4    4  -0.835   0.049   0.645
    1M23     B5    5  -1.117   0.167   0.629
    1M23     B6    6  -1.439   0.199   0.338
    1M23     B7    7  -1.334   0.370   0.478
10 10 10

ITPS/M23/PyCGTool/0000755174611600001440000000000014601243145013206 5ustar  gperei01usersITPS/M23/PyCGTool/M23_CG.gro0000750174611600001440000000054014601243145014626 0ustar  gperei01usersGenerated with cgbuilder
7
    1M23     B1    1   0.004   0.100   0.043
    1M23     B2    2  -0.351   0.051   0.307
    1M23     B3    3  -0.622   0.000   0.545
    1M23     B4    4  -0.835   0.049   0.645
    1M23     B5    5  -1.117   0.167   0.629
    1M23     B6    6  -1.439   0.199   0.338
    1M23     B7    7  -1.334   0.370   0.478
10 10 10

ITPS/M23/PyCGTool/M23.itp0000750174611600001440000000225214601240531014260 0ustar  gperei01users[ moleculetype ]
; molname    nrexcl
  M23         1

 [ atoms ]
; nr type resnr residue atom cgnr charge mass  
   1  SC1    0    M23    B1     1     0     
   2   C4    0    M23    B2     2     0 
   3  TC1    0    M23    B3     3     0
   4  TC5    0    M23    B4     4     0   
   5  SC1    0    M23    B5     5     0   
   6  SC3    0    M23    B6     6     0
   7  SC3    0    M23    B7     7     0
  
[bonds]
; i j  funct    length   force.c.
  1 2   1      0.48	1747.77   
  2 3   1      0.36	4198.27
  3 4   1      0.25	15689.34 
  4 5   1      0.29	5214.76
  5 6   1      0.33	8488.05
 
[constraints]
; i j  funct    length  
  6 7   1      0.24	   
  
[angles]
; i     j       k       funct   angle   force_constant
  1     2       3          1     143.13	37.26 
  2     3       4          1     129.77	30 
  3     4       5          1     135     	200     ; puxado pra tras
  4     5       6          1     135.90	350  ; adjusted kf
  5     6       7          1     113.35	300  ; adjusted kf 

[ dihedrals ]
;  i j k m       type   phase  kf  mult
3     4       5    6          2      0.89	2.36 
4     5       6    7          1      29.26	0.85   3

[ exclusions ]
4 5 6 7
5 6 7
6 7
ITPS/M24/0000755174611600001440000000000014601235110011540 5ustar  gperei01usersITPS/M24/Bartender/0000755174611600001440000000000014601243042013451 5ustar  gperei01usersITPS/M24/Bartender/M24.itp0000750174611600001440000000253614601240720014535 0ustar  gperei01users[ moleculetype ]
; molname    nrexcl
  M24         1

 [ atoms ]
; nr type resnr residue atom cgnr charge mass  
   1  C1     0    M24    R1     1     0     
   2  TC5    0    M24    R2     2     0 
   3  SC1    0    M24    R3     3     0
   4  TC5    0    M24    R4     4     0   
   5  SC1    0    M24    R5     5     0   
   6  SC3    0    M24    R6     6     0
   7  N5a    0    M24    R7     7     0

[bonds]
; i j  funct    length   force.c.
  1 2   1      0.413      2630.98 
  2 3   1      0.289     10255.27 
  3 4   1      0.288     11381.21
  4 5   1      0.291      7296.53 
  5 6   1      0.321     14850.54 

[constraints]
; i j  funct    length  
  6 7   1      0.267     34121.98 
  
[angles]
; i     j       k       funct   angle   force_constant
  1     2       3          1     148.86     28.91 
  2     3       4          1     109.46     42.51 
  3     4       5          1     143.79     500 ; rule that if too close to 150, bump by 10 degrees (original was 153), also increased KF so it does not go to 180
  4     5       6          1     126.89     40.79 
  5     6       7          1     135.26     87.69 


[ dihedrals ]
  4     5       6    7          3      2.80 -2.33 -1.44  3.44  0.44  0.82 
  2     3       4    5          3      4.39 -0.49  2.18  0.64 -3.54  2.96 
  3     4       5    6          3      5.86  0.64  2.11 -0.80 -4.48  3.81 


ITPS/M24/Bartender/M24_CG.gro0000750174611600001440000000053714601243042015100 0ustar  gperei01usersGenerated with cgbuilder
7
    1M24     R1    1  -0.063   0.100   0.057
    1M24     R2    2  -0.351   0.050   0.307
    1M24     R3    3  -0.551   0.003   0.534
    1M24     R4    4  -0.829   0.053   0.656
    1M24     R5    5  -1.118   0.178   0.647
    1M24     R6    6  -1.352   0.175   0.818
    1M24     R7    7  -1.503   0.361   0.774
10 10 10
ITPS/M24/Human/0000755174611600001440000000000014601243054012616 5ustar  gperei01usersITPS/M24/Human/M24_CG.gro0000750174611600001440000000053714601243054014245 0ustar  gperei01usersGenerated with cgbuilder
7
    1M24     R1    1  -0.063   0.100   0.057
    1M24     R2    2  -0.351   0.050   0.307
    1M24     R3    3  -0.551   0.003   0.534
    1M24     R4    4  -0.829   0.053   0.656
    1M24     R5    5  -1.118   0.178   0.647
    1M24     R6    6  -1.352   0.175   0.818
    1M24     R7    7  -1.503   0.361   0.774
10 10 10
ITPS/M24/Human/M24.itp0000750174611600001440000000165314601240734013703 0ustar  gperei01users[ moleculetype ]
; molname    nrexcl
  M24         1

 [ atoms ]
; nr type resnr residue atom cgnr charge mass  
   1  C1     0    M24    R1     1     0     
   2  TC5    0    M24    R2     2     0 
   3  SC1    0    M24    R3     3     0
   4  TC5    0    M24    R4     4     0   
   5  SC1    0    M24    R5     5     0   
   6  SC3    0    M24    R6     6     0
   7  N5a    0    M24    R7     7     0

 [bonds]
; i j  funct    length   force.c.
  1 2   1      0.450      7000 
  2 3   1      0.310      9000
  3 4   1      0.300      7500 
  4 5   1      0.300      7500
  5 6	1      0.320      7500
  6 7   1      0.270     20000 
  
 [angles]
 1  2  3	1	175    40
 2  3  4        1       135   100
 3  4  5        1       140   200   
 4  5  6        1       140   200
 5  6  7        1       160   500

[ dihedrals ]
   2 3 4 5        1	180    6     1 
   3 4 5 6        1 	180    10    1
   4 5 6 7        1     180    2     3
   
ITPS/M24/PyCGTool/0000755174611600001440000000000014601243057013211 5ustar  gperei01usersITPS/M24/PyCGTool/M24.itp0000750174611600001440000000227314601240747014276 0ustar  gperei01users[ moleculetype ]
; molname    nrexcl
  M24         1

 [ atoms ]
; nr type resnr residue atom cgnr charge mass  
   1  C1     0    M24    R1     1     0     
   2  TC5    0    M24    R2     2     0 
   3  SC1    0    M24    R3     3     0
   4  TC5    0    M24    R4     4     0   
   5  SC1    0    M24    R5     5     0   
   6  SC3    0    M24    R6     6     0
   7  N5a    0    M24    R7     7     0

[bonds]
; i j  funct    length   force.c.
  1 2   1      0.43	2245.92
  2 3   1      0.30	6384.07
  3 4   1      0.29	5229.09
  4 5   1      0.29	5427.58
  5 6   1      0.31	7683.66
 

[constraints]
; i j  funct    length  
  6 7   1      0.27	 
  
[angles]
; i     j       k       funct   angle   force_constant
  1     2       3          1     151.37	117.13 
  2     3       4          1     131.56	63.68
  3     4       5          1     137.06	200    ; adjusted KF and bumped angle -10 deg
  4     5       6          1     135.94	80.19
  5     6       7          1     139.62	200  ; adjusted KF and bumped angle -10 deg
 


[ dihedrals ]
  2     3       4    5          1     179.64	1.47  1
  3     4       5    6          1    -179.44	1.97  1
  4     5       6    7          1    -175.99	0.99  3
 



ITPS/M24/PyCGTool/M24_CG.gro0000750174611600001440000000053714601243057014640 0ustar  gperei01usersGenerated with cgbuilder
7
    1M24     R1    1  -0.063   0.100   0.057
    1M24     R2    2  -0.351   0.050   0.307
    1M24     R3    3  -0.551   0.003   0.534
    1M24     R4    4  -0.829   0.053   0.656
    1M24     R5    5  -1.118   0.178   0.647
    1M24     R6    6  -1.352   0.175   0.818
    1M24     R7    7  -1.503   0.361   0.774
10 10 10
ITPS/Pomalidomide/0000755174611600001440000000000014601235110013601 5ustar  gperei01usersITPS/Pomalidomide/Bartender/0000755174611600001440000000000014601243615015520 5ustar  gperei01usersITPS/Pomalidomide/Bartender/Pomalidomide_CG.gro0000750174611600001440000000074714601243615021213 0ustar  gperei01usersGenerated with cgbuilder
10
    1M20     B0    1  -0.176   0.084  -0.596
    1M20     B1    2  -0.111   0.247  -0.802
    1M20     B2    3  -0.111   0.377  -0.663
    1M20     B3    4  -0.121   0.358  -0.472
    1M20     B4    5  -0.190   0.158  -0.327
    1M20     B5    6  -0.356   0.178  -0.259
    1M20     B6    7  -0.020   0.120  -0.277
    1M20     B7    8  -0.183   0.134  -0.111
    1M20     B8    9  -0.326   0.129   0.093
    1M20     B9   10   0.030   0.086   0.054
10 10 10
ITPS/Pomalidomide/Bartender/Pomalidomide.itp0000750174611600001440000000370214601235564020645 0ustar  gperei01users[ moleculetype ]
; molname    nrexcl
  M20         1

 [ atoms ]
; nr type resnr residue atom cgnr charge mass  
   1  SC3     0    M20    B0     1  0   66     
   2  TP1a    0    M20    B1     2  0   48   ; nucleobase like
   3  TN5d    0    M20    B2     3  0   0    ; nucleobase like
   4  TP1a    0    M20    B3     4  0   48   ; nucleobase like
   5  TN1     0    M20    B4     5  0        ; aedamer like
   6  TN6a    0    M20    B5     6  0   45   ; aedamer like
   7  TN6a    0    M20    B6     7  0   45   ; aedamer like
   8  TC5e    0    M20    B7     8  0   0
   9  TC5     0    M20    B8     9  0   45
  10  SN6d    0    M20    B9    10  0   63
   
 
[bonds]
; i j  funct    length   force.c.
  1 5   1      0.265     24977.39 
[constraints]
; i j  funct    length  
  1 2   1      0.278     
  1 4   1      0.306  
  2 4   1      0.347   
  5 6   1      0.182     
  5 7   1      0.182    
  6 7   1      0.349    
  6 9   1      0.365     
  7 10  1      0.349     
  9 10  1      0.358     
  6 10  1      0.514     


[ virtual_sitesn ]
; site funct constructing atom indices
   8     1     6   7   10   9
 
[ virtual_sites3 ]
; Site  from               funct   a          b
   3     1    2     4      1      0.690     0.643
  
[ angles ] 
; i   j   k   funct   ref.angle   force_k
  4     1       5          1     57.29    623.30 
  1     5       7          1     107.28    124.49 
  4     1       7          1     66.93     92.53


  
[ dihedrals ]
; i j k l   funct  ref.angle force_k 
  4     1       5    7          3      0.82  2.47  4.33 -28.10 25.44 22.25           

;[ impropers ]
  2     4       1    5          2     180.00     18.22 ; rmsd:     1.17   
  9     10      6    7          2     180.00    137.95 ; rmsd:     0.50   
  5     6       7    10         2     180.00     57.21 ; rmsd:     0.66   

  
[ exclusions ]
; ring #1
1 2 3 4 5
2 3 4 5
3 4 5
; ring #2
5 6 7 8 9 10
6 7 8 9 10
7 8 9 10
8 9 10
9 10

; for proper angles
4 6
4 7
4 5
1 5
1 7
1 6
ITPS/Pomalidomide/PyCGTool/0000755174611600001440000000000014601243626015254 5ustar  gperei01usersITPS/Pomalidomide/PyCGTool/Pomalidomide.itp0000750174611600001440000000364214601235601020372 0ustar  gperei01users[ moleculetype ]
; molname    nrexcl
  M20         1

 [ atoms ]
; nr type resnr residue atom cgnr charge mass  
   1  SC3     0    M20    B0     1  0   66     
   2  TP1a    0    M20    B1     2  0   48   ; nucleobase like
   3  TN5d    0    M20    B2     3  0   0    ; nucleobase like
   4  TP1a    0    M20    B3     4  0   48   ; nucleobase like
   5  TN1     0    M20    B4     5  0        ; aedamer like
   6  TN6a    0    M20    B5     6  0   45   ; aedamer like
   7  TN6a    0    M20    B6     7  0   45   ; aedamer like
   8  TC5e    0    M20    B7     8  0   0
   9  TC5     0    M20    B8     9  0   45
  10  SN6d    0    M20    B9    10  0   63
   
 
[bonds]
; i j  funct    length   force.c.
  1 5   1      0.266	6026.41
[constraints]
; i j  funct    length  
  1 2   1      0.278     
  1 4   1      0.307  
  2 4   1      0.347 
  5 6   1      0.182     
  5 7   1      0.182    
  6 7   1      0.349    
  6 9   1      0.365     
  7 10  1      0.350     
  9 10  1      0.358     
  6 10  1      0.515     


[ virtual_sitesn ]
; site funct constructing atom indices
   8     1     6   7   10   9
 
[ virtual_sites3 ]
; Site  from               funct   a          b
   3     1    2     4      1      0.690     0.643
  
[ angles ] 
; i   j   k   funct   ref.angle   force_k
  4     1       5          1     56.23     531.55 
  1     5       7          1     106.51    118.20 
  4     1       7          1     62.61     93.23

[ dihedrals ]
; i j k l   funct  ref.angle force_k 
  4     1       5    7          1     -39.11	0.86    2
          
;[ impropers ]
  2     4       1    5          2     145.43     18.08 ; rmsd:     1.17   
  9     10      6    7          2     179.80    135.28 ; rmsd:     0.50   
  5     6       7    10         2     179.23     53.04 ; rmsd:     0.66   

  
[ exclusions ]
; ring #1
1 2 3 4 5
2 3 4 5
3 4 5
; ring #2
5 6 7 8 9 10
6 7 8 9 10
7 8 9 10
8 9 10
9 10

; for proper angles
4 6
4 7
4 5
1 5
1 7
1 6
ITPS/Pomalidomide/PyCGTool/Pomalidomide_CG.gro0000750174611600001440000000074714601243626020747 0ustar  gperei01usersGenerated with cgbuilder
10
    1M20     B0    1  -0.176   0.084  -0.596
    1M20     B1    2  -0.111   0.247  -0.802
    1M20     B2    3  -0.111   0.377  -0.663
    1M20     B3    4  -0.121   0.358  -0.472
    1M20     B4    5  -0.190   0.158  -0.327
    1M20     B5    6  -0.356   0.178  -0.259
    1M20     B6    7  -0.020   0.120  -0.277
    1M20     B7    8  -0.183   0.134  -0.111
    1M20     B8    9  -0.326   0.129   0.093
    1M20     B9   10   0.030   0.086   0.054
10 10 10
ITPS/Pomalidomide/Human/0000755174611600001440000000000014601243623014661 5ustar  gperei01usersITPS/Pomalidomide/Human/Pomalidomide.itp0000750174611600001440000000347014601235551020005 0ustar  gperei01users[ moleculetype ]
; molname    nrexcl
  M20         1

 [ atoms ]
; nr type resnr residue atom cgnr charge mass  
   1  SC3     0    M20    B0     1  0   66     
   2  TP1a    0    M20    B1     2  0   48   ; nucleobase like
   3  TN5d    0    M20    B2     3  0   0    ; nucleobase like
   4  TP1a    0    M20    B3     4  0   48   ; nucleobase like
   5  TN1     0    M20    B4     5  0        ; aedamer like
   6  TN6a    0    M20    B5     6  0   45   ; aedamer like
   7  TN6a    0    M20    B6     7  0   45   ; aedamer like
   8  TC5e    0    M20    B7     8  0   0
   9  TC5     0    M20    B8     9  0   45
  10  SN6d    0    M20    B9    10  0   63
   
 
[bonds]
; i j  funct    length   force.c.
  1 5   1      0.280      8000 
 
[constraints]
; i j  funct    length  
  1 2   1      0.278     
  1 4   1      0.307     
  2 4   1      0.347    
  5 6   1      0.182     
  5 7   1      0.182     
  6 7   1      0.350    
  6 9   1      0.365      
  7 10  1      0.350     
  9 10  1      0.358      
  6 10  1      0.515    

[ virtual_sitesn ]
; site funct constructing atom indices
   8     1     6   7   10   9
 
[ virtual_sites3 ]
; Site  from               funct   a          b
   3     1    2     4      1      0.690     0.643
  
[ angles ] 
; i   j   k   funct   ref.angle   force_k
  4     1       5        1   56.2393  600 
  1     5       7        1   106.505  100 
  4	1	7	 1	60     80

  
[ dihedrals ]
; i j k l   funct  ref.angle force_k 
      4 1 5 7    1    45     7  2            

;[ impropers ]
  2     4       1    5          2     145.463       20 
  9     10      6    7          2     180.00       100 
  5     6       7    10         2     180.00        40 
  
[ exclusions ]
; ring #1
1 2 3 4 5
2 3 4 5
3 4 5
; ring #2
5 6 7 8 9 10
6 7 8 9 10
7 8 9 10
8 9 10
9 10

; for proper angles
4 6
4 7
4 5
1 5
1 7
1 6
ITPS/Pomalidomide/Human/Pomalidomide_CG.gro0000750174611600001440000000074714601243623020354 0ustar  gperei01usersGenerated with cgbuilder
10
    1M20     B0    1  -0.176   0.084  -0.596
    1M20     B1    2  -0.111   0.247  -0.802
    1M20     B2    3  -0.111   0.377  -0.663
    1M20     B3    4  -0.121   0.358  -0.472
    1M20     B4    5  -0.190   0.158  -0.327
    1M20     B5    6  -0.356   0.178  -0.259
    1M20     B6    7  -0.020   0.120  -0.277
    1M20     B7    8  -0.183   0.134  -0.111
    1M20     B8    9  -0.326   0.129   0.093
    1M20     B9   10   0.030   0.086   0.054
10 10 10
ITPS/M25/0000755174611600001440000000000014601235110011541 5ustar  gperei01usersITPS/M25/Human/0000755174611600001440000000000014601241201012607 5ustar  gperei01usersITPS/M25/Human/M25_CG.gro0000750174611600001440000000067114601241201014236 0ustar  gperei01usersGenerated with cgbuilder
9
    1M25     B0    1   0.792   0.047  -0.167
    1M25     B1    2   0.599  -0.039  -0.087
    1M25     B2    3   0.600   0.083  -0.280
    1M25     B3    4   0.344   0.051  -0.169
    1M25     B4    5   0.128   0.100  -0.071
    1M25     B5    6  -0.182   0.089   0.149
    1M25     B6    7  -0.550   0.425   0.384
    1M25     B7    8  -0.345   0.327   0.389
    1M25     B8    9  -0.524   0.216   0.301
10 10 10
ITPS/M25/Human/M25.itp0000750174611600001440000000267114601241110013673 0ustar  gperei01users[ moleculetype ]
; molname    nrexcl
  M25         1

 [ atoms ]
; nr type resnr residue atom cgnr charge mass  
   1  TC5    0    M25    B0     1     0     
   2  TC5    0    M25    B1     2     0 
   3  TC5    0    M25    B2     3     0
   4  TC5    0    M25    B3     4     0   
   5  TC3    0    M25    B4     5     0   
   6  C4     0    M25    B5     6     0
   7  TC5    0    M25    B6     7     0
   8  TC5    0    M25    B7     8     0
   9  TC5    0    M25    B8     9     0
   
[ bonds ]
; i j  funct    length   force.c. 
  3 4   1      0.287         7000
  4 5   1      0.243         7000 
  5 6   1      0.370         5000 
  6 8   1      0.390         2500 
  

[constraints]
; i j  funct    length  
  1 2   1      0.290     
  1 3   1      0.290     
  2 3   1      0.290     
  8 9   1      0.290     
  8 7   1      0.290     
  9 7   1      0.290     

[ angles ]
; i     j       k       funct   angle   force_constant
  2     3       4          1      62	400
  3 	4	5	   1     150	370
  4     5       6	   1     140	 40  
  5 	6	8	   1	 130	 30
  6 	8	9	   1	  70	 70


[ dihedrals ]
; i     j       k    l       funct   phase       kd    pn 
  2     3       4    5          9     0    22	2
  2     3       4    5          9     50   58	1
  2     3       4    5          9    -50   58	1
  4     3       1    2          2     0   100 
  6     8       9    7          2   180    30
  
 [ exclusions ]
 1 2 3 4
 2 3 4
 3 4
  
 6 7 8 9
 7 8 9
 8 9
ITPS/M25/PyCGTool/0000755174611600001440000000000014601241172013206 5ustar  gperei01usersITPS/M25/PyCGTool/M25_CG.gro0000750174611600001440000000067114601241172014635 0ustar  gperei01usersGenerated with cgbuilder
9
    1M25     B0    1   0.792   0.047  -0.167
    1M25     B1    2   0.599  -0.039  -0.087
    1M25     B2    3   0.600   0.083  -0.280
    1M25     B3    4   0.344   0.051  -0.169
    1M25     B4    5   0.128   0.100  -0.071
    1M25     B5    6  -0.182   0.089   0.149
    1M25     B6    7  -0.550   0.425   0.384
    1M25     B7    8  -0.345   0.327   0.389
    1M25     B8    9  -0.524   0.216   0.301
10 10 10
ITPS/M25/PyCGTool/M25.itp0000750174611600001440000000275314601241123014270 0ustar  gperei01users[ moleculetype ]
; molname    nrexcl
  M25         1

 [ atoms ]
; nr type resnr residue atom cgnr charge mass  
   1  TC5    0    M25    B0     1     0     
   2  TC5    0    M25    B1     2     0 
   3  TC5    0    M25    B2     3     0
   4  TC5    0    M25    B3     4     0   
   5  TC3    0    M25    B4     5     0   
   6  C4     0    M25    B5     6     0
   7  TC5    0    M25    B6     7     0
   8  TC5    0    M25    B7     8     0
   9  TC5    0    M25    B8     9     0
   
[bonds]
; i j  funct    length   force.c. 
  3 4   1      0.29	5085.83
  4 5   1      0.24	16700.99
  5 6   1      0.36	4094.35
  6 8   1      0.38	1869.69
  
[constraints]
; i j  funct    length  
  1 2   1      0.29    
  1 3   1      0.29     
  2 3   1      0.29       
  8 9   1      0.29       
  7 8   1      0.29       
  7 9   1      0.29     
  
[ angles ]
; i     j       k       funct   angle   force_constant
  2     3       4          1     60.12	        192.66
  3     4       5          1     146.87	241.95    ; may need adjust
  4     5       6          1     133.58	29.71     ; may need adjusts
  5     6       8          1     127.21	20.42     ; may need adjusts
  6     8       9          1     67.92 	56.76



[ dihedrals ]
; i     j       k    l       funct   phase       kd    pn 
  2     3       4    5          1     0.86	8.97   2 
  4     3       1    2          2     0.02	137.01   
  6     8       9    7          2    179.67	11.94 

  
 [ exclusions ]
 1 2 3 4
 2 3 4
 3 4
  
 6 7 8 9
 7 8 9
 8 9
ITPS/M25/Bartender/0000755174611600001440000000000014601241213013450 5ustar  gperei01usersITPS/M25/Bartender/M25.itp0000750174611600001440000000345614601241075014545 0ustar  gperei01users[ moleculetype ]
; molname    nrexcl
  M25         1

 [ atoms ]
; nr type resnr residue atom cgnr charge mass  
   1  TC5    0    M25    B0     1     0     
   2  TC5    0    M25    B1     2     0 
   3  TC5    0    M25    B2     3     0
   4  TC5    0    M25    B3     4     0   
   5  TC3    0    M25    B4     5     0   
   6  C4     0    M25    B5     6     0
   7  TC5    0    M25    B6     7     0
   8  TC5    0    M25    B7     8     0
   9  TC5    0    M25    B8     9     0
   
[bonds]
; i j  funct    length   force.c. 
  3 4   1      0.286      6291.74 ; rmsd:     2.01
  5 6   1      0.347      5844.18 ; rmsd:     1.78
  6 8   1      0.375      2556.51 ; rmsd:     1.98
[constraints]
; i j  funct    length  
  1 2   1      0.287    
  1 3   1      0.288    
  2 3   1      0.288     
  8 9   1      0.289     
  7 8   1      0.288     
  7 9   1      0.288    
  4 5   1      0.245       ; BT predicts as this, not sure.
  
[ angles ]
; i     j       k       funct   angle   force_constant
  2     3       4          1     60.62    462.80 ; rmsd:     6.30
  3     4       5          1     137.80   370  ; increased KF, dropped 10 deg - this is a problematic angle.  - only thing i did was increase kf a bit too much and bump it down 10 deg
  4     5       6          1     136.85     30 ; increased KF, was too low
  5     6       8          1     131.46     30 ; increased KF, was too low 
  6     8       9          1     68.26     65.58 ; rmsd:     2.34


[ dihedrals ]
; i     j       k    l       funct   phase       kd    pn 
  2     3       4    5          1     152.39      9.03   2 ; rmsd:     0.28
  4     3       1    2          2      0.00    152.35 ; rmsd:     0.77   
  6     8       9    7          2     180.00     67.03 ; rmsd:     1.72   

  
 [ exclusions ]
 1 2 3 4
 2 3 4
 3 4
  
 6 7 8 9
 7 8 9
 8 9
ITPS/M25/Bartender/M25_CG.gro0000750174611600001440000000067114601241213015077 0ustar  gperei01usersGenerated with cgbuilder
9
    1M25     B0    1   0.792   0.047  -0.167
    1M25     B1    2   0.599  -0.039  -0.087
    1M25     B2    3   0.600   0.083  -0.280
    1M25     B3    4   0.344   0.051  -0.169
    1M25     B4    5   0.128   0.100  -0.071
    1M25     B5    6  -0.182   0.089   0.149
    1M25     B6    7  -0.550   0.425   0.384
    1M25     B7    8  -0.345   0.327   0.389
    1M25     B8    9  -0.524   0.216   0.301
10 10 10
ITPS/PEF/0000755174611600001440000000000014601235110011610 5ustar  gperei01usersITPS/PEF/Human/0000755174611600001440000000000014601243423012666 5ustar  gperei01usersITPS/PEF/Human/PEF.itp0000750174611600001440000000377314601236352014031 0ustar  gperei01users[ moleculetype ]
; molname    nrexcl
  PEF         1

 [ atoms ]
; nr type resnr residue atom cgnr charge mass  
   1  TP1     0    PEF    B0     1     0     
   2  N4a     0    PEF    B1     2     0 
   3  TN2a    0    PEF    B2     3     0
   4  TC5     0    PEF    B3     4     0   
   5  TC5     0    PEF    B4     5     0   
   6  N4a     0    PEF    B5     6     0
   7  N4a     0    PEF    B6     7     0
   8  TN2a    0    PEF    B7     8     0
   9  TC5     0    PEF    B8     9     0
   10 TC5     0    PEF    B9     10    0
   11 N4a     0    PEF    B10    11    0
   12 TP1     0    PEF    B11    12    0   

[ bonds ]  
; i j  funct    length   force.c.
  1 2   1      0.276      7500 
  2 4   1      0.347      9500 
  5 6   1      0.347     11000 
  6 7   1      0.297      5000 
  7 9   1      0.346     11000 
 10 11  1      0.344     11000 
 11 12  1      0.275      7500
 
[constraints]
; i j  funct    length 
  3 4   1      0.225     
  3 5   1      0.225     
  4 5   1      0.211     
  8 9   1      0.225     
  8 10  1      0.225     
  9 10  1      0.210     

[angles]
; i     j       k       funct   angle   force_constant
   1     2       4           1     115      90 
   2     4       3           1      80     200 
   3     5       6           1      80     200 
   5     6       7          10     114      65 
   6     7       9          10     114      65 
   7     9       8           1      80     200  
   8     10      11          1      80     200  
  10     11      12          1     115      90 
 
[ dihedrals ]
; i j k l   funct  ref.angle force_k 
  1 	2	4    3		 1	180	 3      2
  8    10      11   12          1	180	 3      2 
  5     6       7    9          2         0     2       
  3     4       5    2          2         0     65 
  3     4       5    6          2         0     65   
  8     9       10   11         2         0     65  
  8     9       10   7          2         0     65

[ exclusions ]

1 2 3 4
2 3 4
3 4

3 5 6 7
5 6 7
6 7


7 8 9 10 
8 9 10
8 9

8 9 10 11
9 10 11
10 11 

ITPS/PEF/Human/PEF_CG.gro0000750174611600001440000000110114601243423014351 0ustar  gperei01usersGenerated with cgbuilder
12
    1PEF     B0    1  -0.473   0.727   0.615
    2PEF     B1    2  -0.425   0.894   0.466
    3PEF     B2    3  -0.300   0.882   0.149
    4PEF     B3    4  -0.520   0.914   0.115
    5PEF     B4    5  -0.391   0.931  -0.052
    6PEF     B5    6  -0.022   0.911  -0.059
    7PEF     B6    7   0.146   0.699  -0.073
    8PEF     B7    8   0.110   0.425   0.145
    9PEF     B8    9   0.317   0.501   0.186
   10PEF     B9   10   0.254   0.326   0.287
   11PEF    B10   11  -0.042   0.129   0.217
   12PEF    B11   12   0.007   0.105  -0.039
10 10 10
ITPS/PEF/PyCGTool/0000755174611600001440000000000014601243426013261 5ustar  gperei01usersITPS/PEF/PyCGTool/PEF.itp0000750174611600001440000000415014601236424014407 0ustar  gperei01users[ moleculetype ]
; molname    nrexcl
  PEF         1

 [ atoms ]
; nr type resnr residue atom cgnr charge mass  
   1  TP1     0    PEF    B0     1     0     
   2  N4a     0    PEF    B1     2     0 
   3  TN2a    0    PEF    B2     3     0
   4  TC5     0    PEF    B3     4     0   
   5  TC5     0    PEF    B4     5     0   
   6  N4a     0    PEF    B5     6     0
   7  N4a     0    PEF    B6     7     0
   8  TN2a    0    PEF    B7     8     0
   9  TC5     0    PEF    B8     9     0
   10 TC5     0    PEF    B9     10    0
   11 N4a     0    PEF    B10    11    0
   12 TP1     0    PEF    B11    12    0   

[bonds]
; i j  funct    length   force.c.
  1 2   1      0.28	5247.18
  2 4   1      0.35	6168.38
  5 6   1      0.35	5689.23
  6 7   1      0.30	2450.51
  7 9   1      0.35	5509.40
 10 11  1      0.34	6014.23
 11 12  1      0.27	5552.56

[constraints]
; i j  funct    length  

  3 4   1         0.22
  3 5   1         0.23
  4 5   1         0.21
  8 9   1         0.23
  8 10  1         0.22 
  9 10  1         0.21


[angles]
; i     j       k       funct   angle   force_constant
  1     2       4          1     123.75    50.31
  2     4       3          1     78.79	   200    ; adjusted, as it was crashing
  3     5       6          1     78.25	   200    ; adjusted, as it was crashing
  5     6       7          1     113.64    43.58
  6     7       9          1     112.98    42.89
  7     9       8          1     78.98	    200   ; adjusted, as it was crashing
  8     10      11         1     79.91	    200   ; adjusted, as it was crashing
 10     11      12         1     121.55     45.28


 
[ dihedrals ]
; i j k l   funct  ref.angle force_k 
  1     2       4    3          1      -178.49	0.83  3
  8     10      11   12         1      -174.81	0.76  3
  
  5     6       7    9          2       0.30	3.15
  3     4       5    2          2       0.07	65.59 
  3     4       5    6          2       0.00	64.12
  8     9       10   11         2       0.00	63.44  
  8     9       10   7          2       0.05	60.81

[ exclusions ]

1 2 3 4
2 3 4
3 4

3 5 6 7
5 6 7
6 7


7 8 9 10 
8 9 10
8 9

8 9 10 11
9 10 11
10 11 

ITPS/PEF/PyCGTool/PEF_CG.gro0000750174611600001440000000110114601243426014744 0ustar  gperei01usersGenerated with cgbuilder
12
    1PEF     B0    1  -0.473   0.727   0.615
    2PEF     B1    2  -0.425   0.894   0.466
    3PEF     B2    3  -0.300   0.882   0.149
    4PEF     B3    4  -0.520   0.914   0.115
    5PEF     B4    5  -0.391   0.931  -0.052
    6PEF     B5    6  -0.022   0.911  -0.059
    7PEF     B6    7   0.146   0.699  -0.073
    8PEF     B7    8   0.110   0.425   0.145
    9PEF     B8    9   0.317   0.501   0.186
   10PEF     B9   10   0.254   0.326   0.287
   11PEF    B10   11  -0.042   0.129   0.217
   12PEF    B11   12   0.007   0.105  -0.039
10 10 10
ITPS/PEF/Bartender/0000755174611600001440000000000014601243416013526 5ustar  gperei01usersITPS/PEF/Bartender/PEF.itp0000750174611600001440000000455214601236337014666 0ustar  gperei01users[ moleculetype ]
; molname    nrexcl
  PEF         1

 [ atoms ]
; nr type resnr residue atom cgnr charge mass  
   1  TP1     0    PEF    B0     1     0     
   2  N4a     0    PEF    B1     2     0 
   3  TN2a    0    PEF    B2     3     0
   4  TC5     0    PEF    B3     4     0   
   5  TC5     0    PEF    B4     5     0   
   6  N4a     0    PEF    B5     6     0
   7  N4a     0    PEF    B6     7     0
   8  TN2a    0    PEF    B7     8     0
   9  TC5     0    PEF    B8     9     0
   10 TC5     0    PEF    B9     10    0
   11 N4a     0    PEF    B10    11    0
   12 TP1     0    PEF    B11    12    0   


[bonds]
; i j  funct    length   force.c.
  1 2   1      0.271      6524.05 ; rmsd:     1.59
  2 4   1      0.340     23232.45 ; rmsd:     1.29
  5 6   1      0.341     21850.38 ; rmsd:     1.38
  6 7   1      0.317      2831.42 ; rmsd:     0.99
  7 9   1      0.341     22138.50 ; rmsd:     1.36
 10 11  1      0.340     23792.55 ; rmsd:     1.10
 11 12  1      0.270      7080.00 ; rmsd:     1.56
[constraints]
; i j  funct    length  

  3 4   1      0.225     
  3 5   1      0.225    
  4 5   1      0.212    
  8 9   1      0.225     
  8 10  1      0.225     
  9 10  1      0.211     


[angles]
; i     j       k       funct   angle   force_constant
  1     2       4          1     117.56     79.28 ; rmsd:     1.53
  2     4       3          1     81.17    200.44 ; rmsd:     5.27
  3     5       6          1     80.65    185.15 ; rmsd:     5.62
  5     6       7          1     113.51     49.93 ; rmsd:     1.77
  6     7       9          1     112.51     50.21 ; rmsd:     1.81
  7     9       8          1     80.59    177.81 ; rmsd:     5.58
  8     10      11         1     81.23    192.06 ; rmsd:     5.10
 10     11      12         1     116.31    101.05 ; rmsd:     1.48

 
[ dihedrals ]
; i j k l   funct  ref.angle force_k 
  1     2       4    3          3      2.25 -4.13  6.77 14.42 -8.83 -10.03 
  8     10      11   12         3      2.51 -4.21  5.95 13.67 -8.50 -9.44 
  5     6       7    9          2      0.00      3.58      
  3     4       5    2          2      0.00     56.21    
  3     4       5    6          2      0.00     54.33 
  8     9       10   11         2      0.00     55.15   
  8     9       10   7          2      0.00     52.92  


[ exclusions ]

1 2 3 4
2 3 4
3 4

3 5 6 7
5 6 7
6 7


7 8 9 10 
8 9 10
8 9

8 9 10 11
9 10 11
10 11 

ITPS/PEF/Bartender/PEF_CG.gro0000750174611600001440000000110114601243416015211 0ustar  gperei01usersGenerated with cgbuilder
12
    1PEF     B0    1  -0.473   0.727   0.615
    2PEF     B1    2  -0.425   0.894   0.466
    3PEF     B2    3  -0.300   0.882   0.149
    4PEF     B3    4  -0.520   0.914   0.115
    5PEF     B4    5  -0.391   0.931  -0.052
    6PEF     B5    6  -0.022   0.911  -0.059
    7PEF     B6    7   0.146   0.699  -0.073
    8PEF     B7    8   0.110   0.425   0.145
    9PEF     B8    9   0.317   0.501   0.186
   10PEF     B9   10   0.254   0.326   0.287
   11PEF    B10   11  -0.042   0.129   0.217
   12PEF    B11   12   0.007   0.105  -0.039
10 10 10
ITPS/M22/0000755174611600001440000000000014601235110011536 5ustar  gperei01usersITPS/M22/PyCGTool/0000755174611600001440000000000014601243342013204 5ustar  gperei01usersITPS/M22/PyCGTool/M22.itp0000750174611600001440000000133114601237742014265 0ustar  gperei01users[ moleculetype ]
; molname    nrexcl
  M22         1

 [ atoms ]
; nr type resnr residue atom cgnr charge mass  
   1  SC1    0    M22    R1     1     0     
   2   C4    0    M22    R2     2     0 
   3   C4    0    M22    R3     3     0
   4  TC1    0    M22    R4     4     0   
   5  SP2    0    M22    R5     5     0     

  
[bonds]
; i j  funct    length   force.c.
  1 2   1      0.42	3141.14
  2 3   1      0.44	1358.06
  3 4   1      0.35	4041.95
  4 5   1      0.28	15408.01
[constraints]
; i j  funct    length  
[angles]
; i     j       k       funct   angle   force_constant
  1     2       3          1     149.73	71.37
  2     3       4          1     125.68	18.61
  3     4       5          1     119.27	17.77


ITPS/M22/PyCGTool/M22_CG.gro0000750174611600001440000000040514601243342014623 0ustar  gperei01usersGenerated with cgbuilder
5
    1M22     R1    1   0.004   0.100   0.043
    1M22     R2    2  -0.353   0.051   0.307
    1M22     R3    3  -0.693   0.052   0.637
    1M22     R4    4  -0.968   0.104   0.871
    1M22     R5    5  -1.172   0.106   0.999
10 10 10
ITPS/M22/Human/0000755174611600001440000000000014601243337012620 5ustar  gperei01usersITPS/M22/Human/M22.itp0000750174611600001440000000143014601237723013674 0ustar  gperei01users[ moleculetype ]
; molname    nrexcl
  M22         1

 [ atoms ]
; nr type resnr residue atom cgnr charge mass  
   1  SC1    0    M22    R1     1     0     
   2   C4    0    M22    R2     2     0 
   3   C4    0    M22    R3     3     0
   4  TC1    0    M22    R4     4     0   
   5  SP2    0    M22    R5     5     0     

  
[bonds]
; i j  funct    length   force.c.
  1 2   1      0.417      4000 ; rmsd:     1.59
  2 3   1      0.470      6000 ; rmsd:     1.80
  3 4   1      0.353      4500 ; rmsd:     1.81
  4 5   1      0.280     10000 ; rmsd:     2.19
 
[ angles ] 
; i   j   k   funct   ref.angle   force_k
  1     2       3          1     160        50 
  2     3       4          1     130        20 
  3     4       5          1     120        20 
 
 
[exclusions]
1 2 3 4 5
ITPS/M22/Human/M22_CG.gro0000750174611600001440000000040514601243337014237 0ustar  gperei01usersGenerated with cgbuilder
5
    1M22     R1    1   0.004   0.100   0.043
    1M22     R2    2  -0.353   0.051   0.307
    1M22     R3    3  -0.693   0.052   0.637
    1M22     R4    4  -0.968   0.104   0.871
    1M22     R5    5  -1.172   0.106   0.999
10 10 10
ITPS/M22/Bartender/0000755174611600001440000000000014601243331013450 5ustar  gperei01usersITPS/M22/Bartender/M22_CG.gro0000750174611600001440000000040514601243331015067 0ustar  gperei01usersGenerated with cgbuilder
5
    1M22     R1    1   0.004   0.100   0.043
    1M22     R2    2  -0.353   0.051   0.307
    1M22     R3    3  -0.693   0.052   0.637
    1M22     R4    4  -0.968   0.104   0.871
    1M22     R5    5  -1.172   0.106   0.999
10 10 10
ITPS/M22/Bartender/M22.itp0000750174611600001440000000222314601237704014532 0ustar  gperei01users[ moleculetype ]
; molname    nrexcl
  M22         1

 [ atoms ]
; nr type resnr residue atom cgnr charge mass  
   1  SC1    0    M22    R1     1     0     
   2   C4    0    M22    R2     2     0 
   3   C4    0    M22    R3     3     0
   4  TC1    0    M22    R4     4     0   
   5  SP2    0    M22    R5     5     0     

  
[bonds]
; i j  funct    length   force.c.
  1 2   1      0.423      3021.51    
  2 3   1      0.426      2550.39 ; rmsd:     2.93
  3 4   1      0.348      5632.72 ; rmsd:     1.76
  4 5   1      0.272     18016.96 ; rmsd:     1.38
[constraints]
; i j  funct    length  
[angles]
; i     j       k       funct   angle   force_constant
  1     2       3          1     158.37     25.50 ; rmsd:     1.46
  2     3       4          1     128.51     16.47 ; rmsd:     2.22
  3     4       5          1     125.58     24.62 ; rmsd:     0.93

[ dihedrals ]
; i j k l   funct  ref.angle force_k 
 ; 1     2       3    4          3      2.25  2.49 -0.83 -0.25  0.54 -0.28 ;; Ryckaert-Belleman's potential. rmsd:     0.01 
 ; 2     3       4    5          3      0.86  1.40  0.46 -0.89 -0.48  0.37 ;; Ryckaert-Belleman's potential. rmsd:     0.03 
ITPS/Pitolisant/0000755174611600001440000000000014601235110013324 5ustar  gperei01usersITPS/Pitolisant/Human/0000755174611600001440000000000014601243561014405 5ustar  gperei01usersITPS/Pitolisant/Human/Pitolisant.itp0000750174611600001440000000254414601235770017257 0ustar  gperei01users[ moleculetype ]
; molname    nrexcl
  PITO         1

 [ atoms ]
; nr type resnr residue atom cgnr charge mass  
   1  SC3    0    PITO    B0     1     0     
   2  SN3a   0    PITO    B1     2     0 
   3  TC1    0    PITO    B2     3     0
   4  SN3a   0    PITO    B3     4     0   
   5  TC1    0    PITO    B4     5     0   
   6  TC5    0    PITO    B5     6     0
   7  TC5    0    PITO    B6     7     0
   8  SX3    0    PITO    B7     8     0

   
[bonds]
; i j  funct    length   force.c.
  2 3   1      0.252     11000   ; AA-mapped
  3 4   1      0.320      9500   ; AA-mapped - stretched
  4 5   1      0.310      7000   ; AA-mapped
  5 6   1      0.320      6000   ; AA-mapped
  5 7   1      0.320      6000   ; AA-mapped 

[constraints]
; i j  funct    length  
  1 2   1      0.227     
  6 7   1      0.275        ; chbenze-definition
  6 8   1      0.321        ; chbenze-definition
  7 8   1      0.321        ; chbenze-definition


[angles]
; i     j       k       funct   angle   force_constant
  1     2       3          1     128     40    
  2     3       4          1     173     70 
  3     4       5          1     134     50 
  4     5       7          1     160     50 
  5     6       7          1     64      45
  
[ dihedrals ]
; i j k l   funct  ref.angle force_k 
   5     7       6    8          2      175    50 

[ exclusions ]

6 7 8
7 8


ITPS/Pitolisant/Human/Pitolisant_CG.gro0000750174611600001440000000061414601243561017614 0ustar  gperei01usersGenerated with cgbuilder
8
    PITO     B0    1  -0.114  -0.781   0.542
    PITO     B1    2  -0.019  -0.671   0.367
    PITO     B2    3   0.080  -0.472   0.258
    PITO     B3    4   0.169  -0.248   0.049
    PITO     B4    5   0.151   0.050  -0.067
    PITO     B5    6   0.211   0.331  -0.069
    PITO     B6    7   0.028   0.278  -0.193
    PITO     B7    8   0.066   0.502  -0.136
10 10 10
ITPS/Pitolisant/PyCGTool/0000755174611600001440000000000014601243564015000 5ustar  gperei01usersITPS/Pitolisant/PyCGTool/Pitolisant.itp0000750174611600001440000000222014601236007017630 0ustar  gperei01users[ moleculetype ]
; molname    nrexcl
  PITO         1

 [ atoms ]
; nr type resnr residue atom cgnr charge mass  
   1  SC3    0    PITO    B0     1     0     
   2  SN3a   0    PITO    B1     2     0 
   3  TC1    0    PITO    B2     3     0
   4  SN3a   0    PITO    B3     4     0   
   5  TC1    0    PITO    B4     5     0   
   6  TC5    0    PITO    B5     6     0
   7  TC5    0    PITO    B6     7     0
   8  SX3    0    PITO    B7     8     0

   
[bonds]
; i j  funct    length   force.c.
  2 3   1      0.25	12392.35 
  3 4   1      0.31	8015.11
  4 5   1      0.31	6311.72
  5 6   1      0.32	9263.66
  5 7   1      0.32	9184.69

 
[constraints]
; i j  funct    length  
  1 2   1      0.23     
  6 7   1      0.28    
  6 8   1      0.32     
  7 8   1      0.32     


[angles]
; i     j       k       funct   angle   force_constant
  1     2       3          1     128.25	25.50
  2     3       4          1     163.69	200
  3     4       5          1     133.72	74.15
  4     5       7          1     141.34	100


  
[ dihedrals ]
; i j k l   funct  ref.angle force_k 
  5     7       6    8          2    179.90	48.80
  
[ exclusions ]

6 7 8
7 8


ITPS/Pitolisant/PyCGTool/Pitolisant_CG.gro0000750174611600001440000000061414601243565020210 0ustar  gperei01usersGenerated with cgbuilder
8
    PITO     B0    1  -0.114  -0.781   0.542
    PITO     B1    2  -0.019  -0.671   0.367
    PITO     B2    3   0.080  -0.472   0.258
    PITO     B3    4   0.169  -0.248   0.049
    PITO     B4    5   0.151   0.050  -0.067
    PITO     B5    6   0.211   0.331  -0.069
    PITO     B6    7   0.028   0.278  -0.193
    PITO     B7    8   0.066   0.502  -0.136
10 10 10
ITPS/Pitolisant/Bartender/0000755174611600001440000000000014601243550015241 5ustar  gperei01usersITPS/Pitolisant/Bartender/Pitolisant.itp0000750174611600001440000000254714601235714020116 0ustar  gperei01users[ moleculetype ]
; molname    nrexcl
  PITO         1

 [ atoms ]
; nr type resnr residue atom cgnr charge mass  
   1  SC3    0    PITO    B0     1     0     
   2  SN3a   0    PITO    B1     2     0 
   3  TC1    0    PITO    B2     3     0
   4  SN3a   0    PITO    B3     4     0   
   5  TC1    0    PITO    B4     5     0   
   6  TC5    0    PITO    B5     6     0
   7  TC5    0    PITO    B6     7     0
   8  SX3    0    PITO    B7     8     0

   
[bonds]
; i j  funct    length   force.c.
  2 3   1      0.240     19162.39 ; rmsd:     1.10
  3 4   1      0.292      8554.18 ; rmsd:     2.65
  4 5   1      0.296      6410.88 ; rmsd:     1.94
  5 6   1      0.321     11315.91 ; rmsd:     1.41
  5 7   1      0.321     11385.20 ; rmsd:     1.40
  
[constraints]
; i j  funct    length  
  1 2   1      0.228     
  6 7   1      0.275    
  6 8   1      0.321     
  7 8   1      0.321     


[angles]
; i     j       k       funct   angle   force_constant
  1     2       3          1     141.72    105.42 
  2     3       4          1     166.61     86.55 
  3     4       5          1     131.58     44.20 
  4     5       7          1     139.62     100 ; too low kf
  5     6       7          1     65.07    200 ; too large 

  
[ dihedrals ]
; i j k l   funct  ref.angle force_k 
  5     7       6    8          2     180.00    134.41 
  
[ exclusions ]

6 7 8
7 8


ITPS/Pitolisant/Bartender/Pitolisant_CG.gro0000750174611600001440000000061414601243550020450 0ustar  gperei01usersGenerated with cgbuilder
8
    PITO     B0    1  -0.114  -0.781   0.542
    PITO     B1    2  -0.019  -0.671   0.367
    PITO     B2    3   0.080  -0.472   0.258
    PITO     B3    4   0.169  -0.248   0.049
    PITO     B4    5   0.151   0.050  -0.067
    PITO     B5    6   0.211   0.331  -0.069
    PITO     B6    7   0.028   0.278  -0.193
    PITO     B7    8   0.066   0.502  -0.136
10 10 10
ITPS/M21/0000755174611600001440000000000014601235110011535 5ustar  gperei01usersITPS/M21/Bartender/0000755174611600001440000000000014601243360013451 5ustar  gperei01usersITPS/M21/Bartender/M21_CG.gro0000750174611600001440000000040514601243360015067 0ustar  gperei01usersGenerated with cgbuilder
5
    1M21     R1    1  -0.590  -0.518   1.216
    1M21     R2    2  -0.558  -0.216   0.802
    1M21     R3    3  -0.485  -0.045   0.489
    1M21     R4    4  -0.355   0.051   0.305
    1M21     R5    5  -0.063   0.100   0.057
10 10 10
ITPS/M21/Bartender/M21.itp0000750174611600001440000000173214601237333014532 0ustar  gperei01users[ moleculetype ]
; molname    nrexcl
  M21         1

 [ atoms ]
; nr type resnr residue atom cgnr charge mass  
   1   C4    0    M21    R1     1     0     
   2   C1    0    M21    R2     2     0 
   3  TC5    0    M21    R3     3     0
   4  TC5    0    M21    R4     4     0   
   5   C1    0    M21    R5     5     0     

  
[bonds]
; i j  funct    length   force.c.
  1 2   1      0.516      1741.42 
  2 3   1      0.331      5496.02 
  4 5   1      0.395      2766.97
[constraints]
; i j  funct    length  
  3 4   1      0.244     
[angles]
; i     j       k       funct   angle   force_constant
  1     2       3          1     108.15     31.01 
  2     3       4          1     151.34    127.13 
  3     4       5          1     149.01     70.54 


[dihedrals]
; i     j       k    l       funct   phase       kd    pn
  1     2       3    4          3      3.04  2.60 -1.32 -0.65  0.21  0.02 ;; Ryckaert-Belleman's potential. rmsd:     0.04

  
[ exclusions ]

3 4 5
2 3 4
ITPS/M21/Human/0000755174611600001440000000000014601243370012614 5ustar  gperei01usersITPS/M21/Human/M21.itp0000750174611600001440000000166714601237352013704 0ustar  gperei01users[ moleculetype ]
; molname    nrexcl
  M21         1

 [ atoms ]
; nr type resnr residue atom cgnr charge mass  
   1   C4    0    M21    R1     1     0     
   2   C1    0    M21    R2     2     0 
   3  TC5    0    M21    R3     3     0
   4  TC5    0    M21    R4     4     0   
   5   C1    0    M21    R5     5     0     

  
[bonds]
; i j  funct    length   force.c.
  1 2   1      0.560      3000     
  2 3   1      0.341      5000 
  4 5   1      0.411      5000 
  
[constraints]
; i j  funct    length  
  3 4   1      0.248     
 
[ angles ] 
; i   j   k   funct   ref.angle   force_k
  1     2       3          1        150     30
  2     3       4          1        155    110
  3     4       5          1        150     80 
  
[ dihedrals ]
; i j k l   funct  ref.angle force_k 
  1     2       3    4          1       165   2  1
;  2     3       4    5          1     176.87      1.00   2 ; rmsd:     0.12

[ exclusions ]

3 4 5
2 3 4
ITPS/M21/Human/M21_CG.gro0000750174611600001440000000040514601243370014232 0ustar  gperei01usersGenerated with cgbuilder
5
    1M21     R1    1  -0.590  -0.518   1.216
    1M21     R2    2  -0.558  -0.216   0.802
    1M21     R3    3  -0.485  -0.045   0.489
    1M21     R4    4  -0.355   0.051   0.305
    1M21     R5    5  -0.063   0.100   0.057
10 10 10
ITPS/M21/PyCGTool/0000755174611600001440000000000014601243373013207 5ustar  gperei01usersITPS/M21/PyCGTool/M21.itp0000750174611600001440000000157414601237365014275 0ustar  gperei01users[ moleculetype ]
; molname    nrexcl
  M21         1

 [ atoms ]
; nr type resnr residue atom cgnr charge mass  
   1   C4    0    M21    R1     1     0     
   2   C1    0    M21    R2     2     0 
   3  TC5    0    M21    R3     3     0
   4  TC5    0    M21    R4     4     0   
   5   C1    0    M21    R5     5     0     

  
[bonds]
; i j  funct    length   force.c.
  1 2   1      0.54	1472.58 
  2 3   1      0.34	4264.32 
  4 5   1      0.41	2501.22
 
[constraints]
; i j  funct    length  
  3 4   1      0.25
     
[angles]
; i     j       k       funct   angle   force_constant
  1     2       3          1     137.22	41.87 
  2     3       4          1     152.28	523.78 
  3     4       5          1     148.72	225.71


[dihedrals]
; i     j       k    l       funct   phase       kd    pn
  1     2       3    4          1      176.35	1.43    1

  
[ exclusions ]

3 4 5
2 3 4
ITPS/M21/PyCGTool/M21_CG.gro0000750174611600001440000000040514601243373014625 0ustar  gperei01usersGenerated with cgbuilder
5
    1M21     R1    1  -0.590  -0.518   1.216
    1M21     R2    2  -0.558  -0.216   0.802
    1M21     R3    3  -0.485  -0.045   0.489
    1M21     R4    4  -0.355   0.051   0.305
    1M21     R5    5  -0.063   0.100   0.057
10 10 10
ITPS/Thyroxine/0000755174611600001440000000000014601235110013167 5ustar  gperei01usersITPS/Thyroxine/Human/0000755174611600001440000000000014601243670014251 5ustar  gperei01usersITPS/Thyroxine/Human/Thyo_CG.gro0000750174611600001440000000074714601243670016264 0ustar  gperei01usersGenerated with cgbuilder
10
    THYO     B0    1   0.032   0.100   0.087
    THYO     B1    2  -0.225   0.079   0.178
    THYO     B2    3  -0.216  -0.178   0.138
    THYO     B3    4  -0.036  -0.321   0.059
    THYO     B4    5  -0.304  -0.323   0.312
    THYO     B5    6  -0.132  -0.467   0.241
    THYO     B6    7  -0.065  -0.666   0.186
    THYO     B7    8   0.121  -0.815   0.242
    THYO     B8    9  -0.097  -0.743  -0.042
    THYO     B9   10   0.098  -0.885  -0.029
10 10 10
ITPS/Thyroxine/Human/Thyroxine.itp0000750174611600001440000000330114601235311016744 0ustar  gperei01users[ moleculetype ]
; molname    nrexcl
  THYO         1

 [ atoms ]
; nr type resnr residue atom cgnr charge mass  
   1  SP2    0    THYO    B0     1     0     
   2  SN1    0    THYO    B1     2     0 
   3  TC5    0    THYO    B2     3     0
   4  X1     0    THYO    B3     4     0   
   5  X1     0    THYO    B4     5     0   
   6  TN2a   0    THYO    B5     6     0
   7  TC5    0    THYO    B6     7     0
   8  X1     0    THYO    B7     8     0
   9  X1     0    THYO    B8     9     0
  10  TP1    0    THYO    B9    10     0

  
[bonds]
; i j  funct    length   force.c.
  1 2   1      0.266     19000 
  2 3   1      0.255     17000   
  8 10  1      0.276     13000 
 10 9   1      0.270     13000

[constraints]
; i j  funct    length  
  3 4   1      0.339     
  3 5   1      0.339     
  4 5   1      0.485 
  5 6   1      0.258    
  4 6   1      0.258
  6 7   1      0.207          
  7 8   1      0.339     
  7 9   1      0.339      
  8 9   1      0.485  


 [angles]
; i     j       k       funct   angle   force_constant 
  1     2       3          1      88      60
  2     3       4          1     130     70 
  5     6       7          1     107     50
  6     7       9          1     135     400
  6     7      10          1     165     200
  3     6       7          1     135     390
  1     3       6	    1    130     105

[ dihedrals ]
; i j k l   funct  ref.angle force_k 

1     2       3    4          9     -122	 5   3	
1     2       3    4          9      -82	 3   1  
5     6       7    8          1      330 	7   2
      	
3     4       5    6          2     180.00    60    
7     8       9    10         2     180.00    47 

[ exclusions ] 

3 4 5 
4 5 

5 7
4 7 
6 8
6 9

7 8 9 
8 9 


ITPS/Thyroxine/PyCGTool/0000755174611600001440000000000014601243677014650 5ustar  gperei01usersITPS/Thyroxine/PyCGTool/Thyo_CG.gro0000750174611600001440000000074714601243677016663 0ustar  gperei01usersGenerated with cgbuilder
10
    THYO     B0    1   0.032   0.100   0.087
    THYO     B1    2  -0.225   0.079   0.178
    THYO     B2    3  -0.216  -0.178   0.138
    THYO     B3    4  -0.036  -0.321   0.059
    THYO     B4    5  -0.304  -0.323   0.312
    THYO     B5    6  -0.132  -0.467   0.241
    THYO     B6    7  -0.065  -0.666   0.186
    THYO     B7    8   0.121  -0.815   0.242
    THYO     B8    9  -0.097  -0.743  -0.042
    THYO     B9   10   0.098  -0.885  -0.029
10 10 10
ITPS/Thyroxine/PyCGTool/Thyroxine.itp0000750174611600001440000000327014601235340017343 0ustar  gperei01users[ moleculetype ]
; molname    nrexcl
  THYO         1

 [ atoms ]
; nr type resnr residue atom cgnr charge mass  
   1  SP2    0    THYO    B0     1     0     
   2  SN1    0    THYO    B1     2     0 
   3  TC5    0    THYO    B2     3     0
   4  X1     0    THYO    B3     4     0   
   5  X1     0    THYO    B4     5     0   
   6  TN2a   0    THYO    B5     6     0
   7  TC5    0    THYO    B6     7     0
   8  X1     0    THYO    B7     8     0
   9  X1     0    THYO    B8     9     0
  10  TP1    0    THYO    B9    10     0

[bonds]
; i j  funct    length   force.c.
  2 3   1      0.255	17861.524
  8 10  1      0.276	5502.709
 10 9   1      0.270	5289.450

[constraints]
; i j  funct    length  
  1 2   1      0.266	  
  3 4   1      0.339    
  3 5   1      0.339     
  4 5   1      0.485     
  5 6   1      0.258     
  4 6   1      0.258     
  6 7   1      0.207     
  7 8   1      0.339     
  7 9   1      0.339     
  8 9   1      0.485     

[angles]
; i     j       k       funct   angle   force_constant
  1     2       3          1     101.49	26.54 
  2     3       4          1     128.38	167.88 
  5     6       7          1     104.85	80.37 
  6     7       9          1     134.86	108.82
  6     7       10         1     164.85	1500    ;adjusted, over 5000
  3     6       7          1     136.45	916.26
  1     3       6          1     133.52	74.63 


[ dihedrals ]
; i j k l   funct  ref.angle force_k 
  1     2       3    4          1     -86.22	1.23   3 
  5     6       7    8          1     -103.82	0.73   2    	
  3     4       5    6          2     178.28	99.00
  7     8       9    10         2     179.94	72.34  

[ exclusions ] 

3 4 5 
4 5 

5 7
4 7 
6 8
6 9

7 8 9 
8 9 


ITPS/Thyroxine/Bartender/0000755174611600001440000000000014601243662015110 5ustar  gperei01usersITPS/Thyroxine/Bartender/Thyo_CG.gro0000750174611600001440000000074714601243662017123 0ustar  gperei01usersGenerated with cgbuilder
10
    THYO     B0    1   0.032   0.100   0.087
    THYO     B1    2  -0.225   0.079   0.178
    THYO     B2    3  -0.216  -0.178   0.138
    THYO     B3    4  -0.036  -0.321   0.059
    THYO     B4    5  -0.304  -0.323   0.312
    THYO     B5    6  -0.132  -0.467   0.241
    THYO     B6    7  -0.065  -0.666   0.186
    THYO     B7    8   0.121  -0.815   0.242
    THYO     B8    9  -0.097  -0.743  -0.042
    THYO     B9   10   0.098  -0.885  -0.029
10 10 10
ITPS/Thyroxine/Bartender/Thyroxine.itp0000750174611600001440000000352414601235252017615 0ustar  gperei01users[ moleculetype ]
; molname    nrexcl
  THYO         1

 [ atoms ]
; nr type resnr residue atom cgnr charge mass  
   1  SP2    0    THYO    B0     1     0     
   2  SN1    0    THYO    B1     2     0 
   3  TC5    0    THYO    B2     3     0
   4  X1     0    THYO    B3     4     0   
   5  X1     0    THYO    B4     5     0   
   6  TN2a   0    THYO    B5     6     0
   7  TC5    0    THYO    B6     7     0
   8  X1     0    THYO    B7     8     0
   9  X1     0    THYO    B8     9     0
  10  TP1    0    THYO    B9    10     0

[bonds]
; i j  funct    length   force.c.
  2 3   1      0.275     20374.33 ; rmsd:     1.00
  8 10  1      0.273     20099.76 ; rmsd:     1.29
 10 9   1      0.272     18234.57 ; rmsd:     1.31
[constraints]
; i j  funct    length  
  1 2   1      0.265     
  3 4   1      0.339    
  3 5   1      0.339     
  4 5   1      0.485     
  5 6   1      0.258     
  4 6   1      0.258     
  6 7   1      0.207     
  7 8   1      0.339     
  7 9   1      0.339     
  8 9   1      0.485     

[angles]
; i     j       k       funct   angle   force_constant
  1     2       3          1     118.23     77.65 
  2     3       4          1     130.78    122.42 
  5     6       7          1     107.00     92.17 
  6     7       9          1     136.50    170.63
  6     7       10         1     163.97    393.84
  3     6       7          1     136.26    412.31 
  1     3       6          1     145.68    104.28 


[ dihedrals ]
; i j k l   funct  ref.angle force_k 
  1     2       3    4          1     190.02      3.31   3 ; rmsd:     0.78
  5     6       7    8          1     333.51      8.10   2 ; rmsd:     1.75      	
  3     4       5    6          2     180.00     99.61 ; rmsd:     0.57   
  7     8       9    10         2     180.00     81.26 ; rmsd:     0.78   

[ exclusions ] 

3 4 5 
4 5 

5 7
4 7 
6 8
6 9

7 8 9 
8 9