H2OAC

protex/forcefield/file.crd

@@ -0,0 +1,4 @@
+TITLE : Created by VMD with 9 atoms
+   0.014   0.000   5.000  -1.026   0.200   7.000  -0.566   0.260   6.000  -1.689
+  -0.670   6.000  -1.620   1.090   8.000  -0.229   0.430   1.000   1.093  -0.600
+   3.000   1.744  -0.740   3.000   0.473   0.250   1.000

protex/forcefield/file.mol2

@@ -0,0 +1,21 @@
+@<TRIPOS>MOLECULE
+generated by VMD
+    9    0    1    0    0
+SMALL
+NO_CHARGES
+****
+Energy = 0
+
+@<TRIPOS>ATOM
+      1  C1         0.0140    0.0000    5.0000   C1    1  H2OA        0.000000
+      2  C2        -1.0260    0.2000    7.0000   C2    1  H2OA        0.000000
+      3  H1        -0.5660    0.2600    6.0000   H1    1  H2OA        0.000000
+      4  H2        -1.6890   -0.6700    6.0000   H2    1  H2OA        0.000000
+      5  H3        -1.6200    1.0900    8.0000   H3    1  H2OA        0.000000
+      6  O1        -0.2290    0.4300    1.0000   O1    1  H2OA        0.000000
+      7  O2         1.0930   -0.6000    3.0000   O2    1  H2OA        0.000000
+      8  H          1.7440   -0.7400    3.0000    H    1  H2OA        0.000000
+      9  HO1        0.4730    0.2500    1.0000  HO1    1  H2OA        0.000000
+
+@<TRIPOS>SUBSTRUCTURE
+1 ****        1 TEMP                        0 ****  **** 0 ROOT

protex/forcefield/file.pdbx

@@ -0,0 +1,28 @@
+data_file
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.pdbx_formal_charge
+_atom_site.auth_asym_id
+ATOM 1  C1  C1 . H2OA C . 1 ? 0.014000 0.000000 5.000000 9.000000 0.000000 C
+ATOM 2  C2  C2 . H2OA C . 1 ? -1.026000 0.200000 7.000000 20.000000 0.000000 C
+ATOM 3  H1  H1 . H2OA C . 1 ? -0.566000 0.260000 6.000000 13.000000 0.000000 C
+ATOM 4  H2  H2 . H2OA C . 1 ? -1.689000 -0.670000 6.000000 89.000000 0.000000 C
+ATOM 5  H3  H3 . H2OA C . 1 ? -1.620000 1.090000 8.000000 83.000000 0.000000 C
+ATOM 6  O1  O1 . H2OA C . 1 ? -0.229000 0.430000 1.000000 98.000000 0.000000 C
+ATOM 7  O2  O2 . H2OA C . 1 ? 1.093000 -0.600000 3.000000 42.000000 0.000000 C
+ATOM 8  H   H . H2OA C . 1 ? 1.744000 -0.740000 3.000000 75.000000 0.000000 C
+ATOM 9  HO1 HO1 . H2OA C . 1 ? 0.473000 0.250000 1.000000 57.000000 0.000000 C
+#

protex/forcefield/h2oac/initialize.sh

@@ -0,0 +1,7 @@
+#!/bin/bash
+echo "Running packmol..."
+packmol_mod <packmol.inp >packmol.out #to allow for 5character name
+echo "Running pdb2crd..."
+pdb2corv2 small_box_init.pdb >small_box_init.crd #to allow for 5character name
+echo "Running CHARMM, create psf, crd..."
+charmm -i write_psf_crd.inp -o write_psf_crd.out

protex/forcefield/h2oac/packmol.inp

@@ -0,0 +1,31 @@
+tolerance 2.0
+seed -1
+
+
+filetype pdb
+output small_box_init.pdb
+
+structure ../pdb/im1h_min.pdb 
+  number 15
+  inside box -11. -11. -11. 11. 11. 11.
+end structure
+
+structure ../pdb/oac_dummy_min.pdb
+  number 25
+  inside box -11. -11. -11. 11. 11. 11.
+end structure
+
+structure ../pdb/im1_min.pdb 
+  number 35
+  inside box -11. -11. -11. 11. 11. 11.
+end structure
+
+structure ../pdb/hoac_dummy_min.pdb
+  number 35
+  inside box -11. -11. -11. 11. 11. 11.
+end structure
+
+structure ../pdb/h2oac_min.pdb
+  number 10
+  inside box -11. -11. -11. 11. 11. 11.
+end structure

protex/forcefield/h2oac/write_psf_crd.inp

@@ -0,0 +1,83 @@
+*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*~ Minimization of PACKMOL structure
+*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*
+ioformat extended
+!=======================================================================
+! Force field
+!=======================================================================
+!set TOPPAR /site/raid2/florian/str/scaled_lj
+set TOPPAR ../toppar
+stream @TOPPAR/toppar_drude_master_protein_2013f_lj025.str
+stream @TOPPAR/im1h_d.str
+stream @TOPPAR/oac_d_dummy2.str
+stream @TOPPAR/im1_d_dummy.str
+stream @TOPPAR/hoac_d_dummy.str
+stream @TOPPAR/h2oac_d.str
+
+read sequence IM1H 15
+generate IM1H setup warn drude dmass 0.4
+
+read sequence OAC 25
+generate OAC setup warn drude dmass 0.4
+
+read sequence IM1 35
+generate IM1 setup warn drude dmass 0.4
+
+read sequence HOAC 35
+generate HOAC setup warn drude dmass 0.4
+
+read sequence H2OAC 10
+generate H2OAC setup warn drude dmass 0.4
+!=======================================================================
+! Coordinates
+!=======================================================================
+open  unit 10 read form name "./small_box_init.crd"
+read  unit 10 coor card 
+close unit 10
+
+coor sdrude !gives cordinates to drudes
+coor shake !gives cordinates to lonepairs
+
+set XTL = 22.0
+calc XTL2 = @xtl/2
+set GRID = 12
+
+crystal define cubic @XTL @XTL @XTL 90.0 90.0 90.0
+crystal build  cutoff @XTL2 noperations 0
+image byresidue select ALL end
+
+energy  bycb atom vatom cdiel ewal pmew vswitch -
+        ctonnb           10  -
+        ctofnb           11  -
+        cutnb            14  -
+        cutim            14  -
+        kappa           0.41 -
+        fftx          @GRID  -
+        ffty          @GRID  -
+        fftz          @GRID  -
+        spli order        6  -
+        qcor              0  -
+        wmin            1.5  -
+        inbfrq           -1  -
+        imgfrq           -1
+
+shake bonh param tol 1.0e-9 nofast -
+      select ( .not. type D* ) end -
+      select ( .not. type D* ) end
+
+open unit 10 write form name "./small_box.psf"
+write unit 10 psf xplor card
+close unit 10
+
+!=======================================================================
+! Minimization
+!=======================================================================
+mini sd nstep 500
+!mini abnr nstep 3000
+
+open  unit 10 write form name "./small_box.crd"
+write unit 10 coor card 
+close unit 10
+
+

protex/forcefield/pdb/h2oac_min.pdb

@@ -0,0 +1,22 @@
+COMPND    h2oac_min.xyz 
+AUTHOR    GENERATED BY OPEN BABEL 3.1.1
+HETATM    1  C1  H2OAC   1       0.014   0.005   0.009  1.00  0.00           H2OAC  
+HETATM    2  C2  H2OAC   1      -1.026   0.207  -1.020  1.00  0.00           H2OAC  
+HETATM    3  H1  H2OAC   1      -0.566   0.266  -2.013  1.00  0.00           H2OAC  
+HETATM    4  H2  H2OAC   1      -1.689  -0.676  -0.989  1.00  0.00           H2OAC  
+HETATM    5  H3  H2OAC   1      -1.620   1.098  -0.783  1.00  0.00           H2OAC  
+HETATM    6  O1  H2OAC   1       1.093  -0.603  -0.342  1.00  0.00           H2OAC  
+HETATM    7  O2  H2OAC   1      -0.229   0.431   1.198  1.00  0.00           H2OAC  
+HETATM    8  H   H2OAC   1       0.473   0.251   1.857  1.00  0.00           H2OAC  
+HETATM    9  HO1 H2OAC   1       1.744  -0.743   0.375  1.00  0.00           H2OAC  
+CONECT    1    2    6    7                                            
+CONECT    2    3    4    5    1                                       
+CONECT    3    2                                                      
+CONECT    4    2                                                      
+CONECT    5    2                                                      
+CONECT    6    1    9                                                 
+CONECT    7    1    8                                                 
+CONECT    9    6                                                      
+CONECT    8    7                                                      
+MASTER        0    0    0    0    0    0    0    0    9    0    9    0
+END

protex/forcefield/pdb/h2oac_min.xyz

@@ -0,0 +1,12 @@
+9
+
+ C   -1.026174750710    0.207285652090   -1.019590692280
+ C    0.014339540283    0.005370640432    0.008636470843
+ H   -0.565799462392    0.265721492414   -2.013098614578
+ H   -1.688561563317   -0.676092276648   -0.988963447458
+ H   -1.619968889749    1.098204105916   -0.782502483870
+ O    1.092721256273   -0.603033335102   -0.342169440206
+ O   -0.229162246560    0.431151988202    1.198431598365
+ H    1.743970509904   -0.743384488882    0.375388749904
+ H    0.472799759007    0.251370830131    1.856932693829
+

protex/forcefield/pdb/h2oac_test.pdb

@@ -0,0 +1,13 @@
+REMARK  STRUCTURE OPTIMIZATION                                                        
+REMARK   DATE:     5/ 5/20      9:48:22      CREATED BY USER: florian                 
+ATOM      1  C1  H2OAC   1       1.547   1.021   0.071  1.00  0.00      H2OAC
+ATOM      2  C2  H2OAC   1       0.055   1.010   0.285  1.00  0.00      H2OAC
+ATOM      3  H1  H2OAC   1      -0.151   0.705   1.313  1.00  0.00      H2OAC
+ATOM      4  H2  H2OAC   1      -0.400   0.289  -0.396  1.00  0.00      H2OAC
+ATOM      5  H3  H2OAC   1      -0.378   2.003   0.107  1.00  0.00      H2OAC
+ATOM      6  O1  H2OAC   1       2.156   2.222  -0.046  1.00  0.00      H2OAC
+ATOM      7  O2  H2OAC   1       2.222  -0.075   0.027  1.00  0.00      H2OAC
+ATOM      8  H   H2OAC   1       1.548   2.998   0.017  1.00  0.00      H2OAC
+ATOM      9  HO2 H2OAC   1       3.178   0.126  -0.105  1.00  0.00      H2OAC
+TER      10      H2OAC    1
+END

protex/forcefield/pdb/hoac_dummy_min.pdb

@@ -0,0 +1,13 @@
+REMARK  STRUCTURE OPTIMIZATION                                                        
+REMARK   DATE:     5/ 5/20      9:48:22      CREATED BY USER: florian                 
+ATOM      1  C1  HOAC    1       0.014   0.005   0.009  1.00  0.00      HOAC
+ATOM      2  C2  HOAC    1      -1.026   0.207  -1.020  1.00  0.00      HOAC
+ATOM      3  H1  HOAC    1      -0.566   0.266  -2.013  1.00  0.00      HOAC
+ATOM      4  H2  HOAC    1      -1.689  -0.676  -0.989  1.00  0.00      HOAC
+ATOM      5  H3  HOAC    1      -1.620   1.098  -0.783  1.00  0.00      HOAC
+ATOM      6  O1  HOAC    1       1.093  -0.603  -0.342  1.00  0.00      HOAC
+ATOM      7  O2  HOAC    1      -0.229   0.431   1.198  1.00  0.00      HOAC
+ATOM      8  H   HOAC    1       0.473   0.251   1.857  1.00  0.00      HOAC
+ATOM      9  HO1 HOAC    1       1.744  -0.743   0.375  1.00  0.00      HOAC
+TER      10      HOAC     1
+END

protex/forcefield/pdb/hoac_dummy_test.pdb

@@ -0,0 +1,13 @@
+REMARK  STRUCTURE OPTIMIZATION                                                        
+REMARK   DATE:     5/ 5/20      9:48:22      CREATED BY USER: florian                 
+ATOM      1  C1  HOAC    1       1.547   1.021   0.071  1.00  0.00      HOAC
+ATOM      2  C2  HOAC    1       0.055   1.010   0.285  1.00  0.00      HOAC
+ATOM      3  H1  HOAC    1      -0.151   0.705   1.313  1.00  0.00      HOAC
+ATOM      4  H2  HOAC    1      -0.400   0.289  -0.396  1.00  0.00      HOAC
+ATOM      5  H3  HOAC    1      -0.378   2.003   0.107  1.00  0.00      HOAC
+ATOM      6  O1  HOAC    1       2.156   2.222  -0.046  1.00  0.00      HOAC
+ATOM      7  O2  HOAC    1       2.222  -0.075   0.027  1.00  0.00      HOAC
+ATOM      8  H   HOAC    1       1.548   2.998   0.017  1.00  0.00      HOAC
+ATOM      9  HO2 HOAC    1       3.178   0.126  -0.105  1.00  0.00      HOAC
+TER      10      HOAC     1
+END

protex/forcefield/pdb/oac_dummy_min.pdb

@@ -0,0 +1,13 @@
+REMARK  STRUCTURE OPTIMIZATION                                                        
+REMARK   DATE:     5/ 5/20      9:48:22      CREATED BY USER: florian                 
+ATOM      1  C1  OAC     1       0.014   0.005   0.009  1.00  0.00      OAC
+ATOM      2  C2  OAC     1      -1.026   0.207  -1.020  1.00  0.00      OAC
+ATOM      3  H1  OAC     1      -0.566   0.266  -2.013  1.00  0.00      OAC
+ATOM      4  H2  OAC     1      -1.689  -0.676  -0.989  1.00  0.00      OAC
+ATOM      5  H3  OAC     1      -1.620   1.098  -0.783  1.00  0.00      OAC
+ATOM      6  O1  OAC     1       1.093  -0.603  -0.342  1.00  0.00      OAC
+ATOM      7  O2  OAC     1      -0.229   0.431   1.198  1.00  0.00      OAC
+ATOM      8  H   OAC     1       0.473   0.251   1.857  1.00  0.00      OAC
+ATOM      9  HO1 OAC     1       1.744  -0.743   0.375  1.00  0.00      OAC
+TER      10      OAC      1
+END

protex/forcefield/pdb/oac_dummy_test.pdb

@@ -0,0 +1,13 @@
+REMARK  STRUCTURE OPTIMIZATION                                                        
+REMARK   DATE:     5/ 5/20      9:48:22      CREATED BY USER: florian                 
+ATOM      1  C1  OAC     1       1.547   1.021   0.071  1.00  0.00      OAC
+ATOM      2  C2  OAC     1       0.055   1.010   0.285  1.00  0.00      OAC
+ATOM      3  H1  OAC     1      -0.151   0.705   1.313  1.00  0.00      OAC
+ATOM      4  H2  OAC     1      -0.400   0.289  -0.396  1.00  0.00      OAC
+ATOM      5  H3  OAC     1      -0.378   2.003   0.107  1.00  0.00      OAC
+ATOM      6  O1  OAC     1       2.156   2.222  -0.046  1.00  0.00      OAC
+ATOM      7  O2  OAC     1       2.222  -0.075   0.027  1.00  0.00      OAC
+ATOM      8  H   OAC     1       1.548   2.998   0.017  1.00  0.00      OAC
+ATOM      9  HO2 OAC     1       3.178   0.126  -0.105  1.00  0.00      OAC
+TER      10      OAC      1
+END

protex/forcefield/toppar/h2oac_d.str

@@ -0,0 +1,112 @@
+* Toppar stream file generated by FFParam cgenfftoconverter
+* For use with Drude force field
+*
+
+ioformat extended
+
+read rtf card append
+* Topologies generated by FFParam cgenfftoconverter
+* For use with Drude force field
+*
+44
+
+AUTO ANGL DIHE DRUD
+
+! Converts cgenff atomtype to drude atom types.
+! Charges are picked from cgenff stream file
+! Alpha and Thole values are picked from first match of atom type in a text file containing all currently available residues.
+! If it cannot find the values -1.0 and -1.3 values are assigned to the atom type.
+
+!types like OAC, charges not checked, alpha,thole o just averaged from HOAC, c not touched from hoac
+RESI H2OAC          1.000 ! protonated acetic acid
+!
+!  H1      O1-HO1
+!    \    //
+! H2-C2--C1
+!    /     \
+!  H3       O2-H
+GROUP
+ATOM C1   CD2O2A   0.980  ALPHA -1.207 THOLE  0.708
+ATOM C2   CD33A   -0.276  ALPHA -2.114 THOLE  0.750
+ATOM H1   HDA3A    0.092
+ATOM H2   HDA3A    0.092
+ATOM H3   HDA3A    0.092
+ATOM O1   OD2C2A   0.000  ALPHA -1.100 THOLE  1.332
+ATOM O2   OD2C2A   0.000  ALPHA -1.100 THOLE  1.332
+ATOM H    HDP1A    0.370
+ATOM HO1  HDP1A    0.370
+ATOM LPO11 LPD    -0.180
+ATOM LPO12 LPD    -0.180
+ATOM LPO21 LPD    -0.180
+ATOM LPO22 LPD    -0.180
+
+
+BOND C2 C1
+BOND C1 O1
+BOND C1 O2
+BOND C2 H1
+BOND C2 H2
+BOND C2 H3
+BOND O2 H
+BOND O1 HO1
+BOND O1 LPO11
+BOND O1 LPO12
+BOND O2 LPO21
+BOND O2 LPO22
+
+IMPR O1 C2 O2 C1 !analogous to acetate
+
+!LP positions and anistropic polarization from NMA
+LONEPAIR relative LPO11 O1 C1 O2 distance 0.30 angle 91.0 dihe   0.0
+LONEPAIR relative LPO12 O1 C1 O2 distance 0.30 angle 91.0 dihe 180.0
+ANISOTROPY O1 C1 LPO11 LPO12  A11 0.6968  A22 1.2194
+!LP positions and anistropic polarization from MeOH
+LONEPAIR relative LPO21 O2 C1 H  distance 0.35 angle 110.9 dihe  91.0
+LONEPAIR relative LPO22 O2 C1 H  distance 0.35 angle 110.9 dihe 269.0
+ANISOTROPY O2 C1 LPO21 LPO22 A11 0.8108 A22 1.2162
+
+!IC  O1  C1  C2  H1         1.2000  126.00    0.00  109.50   1.1110
+!IC  H   O2  C1  O1         0.9700  110.00    0.00  123.00   1.2000
+!IC  H   O2  C1  C2         0.9700  110.00  180.00  111.00   1.5100
+!IC  O2  C1  C2  H1         1.3300  111.00  180.00  109.50   1.1110
+!IC  O2  C1  C2  H2         1.3300  111.00   60.00  109.50   1.1110
+!IC  O2  C1  C2  H3         1.3300  111.00  -60.00  109.50   1.1110 
+
+END
+
+
+read param card append
+* Parameters generated by FFParam cgenfftoconverter
+* For use with Drude force field
+*
+
+! Parameters are picked from same text file containing all currently available parameters.
+! Similar approach like cgenff is applied, but it is not checked for its robustness.
+
+BONDS
+!CD2O3A   CD33A   110.000  1.535   ! from CD2O2A CD33A  PENALTY  1.000
+!CD2O3A   OD2C1A   623.000  1.239   ! from CD2O4A OD2C1B  PENALTY  2.000
+!CD2O3A   OD31A   150.000  1.330   ! from CD2O3A OD30C  PENALTY  5.000
+OD2C2A    HDP1A    480.40      0.969 ! ACEH, PEML from OD31F HDP1A
+
+ANGLES
+!CD33A   CD2O3A   OD2C1A   20.000  125.000   ! C2-C1-O1 war 23.80 123.00 from CD33A CD2O2A OD2C2A  PENALTY  5.000
+!CD33A   CD2O3A   OD31A   23.600  114.000   ! C2-C1-O2 war 23.80 123.00 from CD33A CD2O2A OD2C2A  PENALTY 11.000
+!OD2C1A   CD2O3A   OD31A   100.000  126.000   ! O1-C1-O2 war 90.00 123.00 from OD2C3A CD2O3A OD30C  PENALTY 11.000
+!CD2O3A   CD33A   HDA3A   27.700  107.500   ! C1-C2-H1/2/3 from CD2O2A CD33A HDA3A  PENALTY  1.000
+!CD2O3A   OD31A   HDP1A   86.000  110.000   ! C1-O2-H war 65.00 108.00 from CD2R6A OD31A HDP1A  PENALTY  7.000
+CD2O2A   OD2C2A    HDP1A     58.90    110.20   15.10   2.3770 ! ACEH, PEML 
+
+DIHEDRALS
+!CD33A   CD2O3A   OD31A   HDP1A   0.990  2  180.000   ! from CD2R6A CD2R6A OD31A HDP1A  PENALTY 29.000
+!OD2C1A   CD2O3A   CD33A   HDA3A   0.420  3  180.000   ! from OD2C2A CD2O2A CD33A HDA3A  PENALTY  6.000
+!OD2C1A   CD2O3A   OD31A   HDP1A   1.110  2  180.000   ! from OD2C3A CD2O3A OD30D HDP1A  PENALTY 30.000
+!OD31A   CD2O3A   CD33A   HDA3A   0.420  3  180.000   ! from OD2C2A CD2O2A CD33A HDA3A  PENALTY 12.000
+HDP1A    OD2C2A    CD2O2A   OD2C2A      1.110    2   180.00 ! from HDP1A OD31F CD2O3A OD2C3A ACEH, PEML 
+HDP1A    OD2C2A    CD2O2A   CD33A       3.760    2   180.00 ! from HDP1A    OD31F    CD2O3A   CD33C       3.760    2   180.00 ! ACEH, PEML 
+
+IMPROPERS
+
+
+END
+RETURN