Merge pull request #87 from florianjoerg/dist_prob

distance-based probabilities, npT ensemble, option to change probability correction factor (K)

protex/forcefield/fora.str

@@ -0,0 +1,75 @@
+* 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.
+
+RESI  FORA     -1.0000
+GROUP
+ATOM C      CD2O2A         0.520  ALPHA   -1.0160  THOLE   0.8990
+ATOM H      HDP1C           0.000
+ATOM O2     OD2C2A         0.000  ALPHA   -0.6990  THOLE   2.3990 ! You may also consider OD2C1C  OD2C3A Equivalent Atomtypes
+ATOM O1     OD2C2A         0.000  ALPHA   -0.6990  THOLE   2.3990 ! You may also consider OD2C1C  OD2C3A Equivalent Atomtypes
+ATOM HO1    DUMH           0.000 
+ATOM LPO21  LPDO1         -0.380
+ATOM LPO22  LPDO1         -0.380
+ATOM LPO11  LPDO1         -0.380
+ATOM LPO12  LPDO1         -0.380
+
+BOND C  H 
+BOND C  O1 
+BOND C  O2 
+BOND O1  HO1 
+BOND  LPO21  O2 
+BOND  LPO22  O2 
+BOND  LPO11  O1 
+BOND  LPO12  O1 
+
+LONE RELATIVE LPO21  O2  C  O1 DIST 0.3500 ANGLE  110.00 DIHE    0.00
+LONE RELATIVE LPO22  O2  C  O1 DIST 0.3500 ANGLE  110.00 DIHE  180.00
+LONE RELATIVE LPO11  O1  C  O2 DIST 0.3500 ANGLE  110.00 DIHE    0.00
+LONE RELATIVE LPO12  O1  C  O2 DIST 0.3500 ANGLE  110.00 DIHE  180.00
+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
+CD2O2A   HDP1C   310.000  1.104   ! from CD2O1C HDP1C  PENALTY  2.000
+OD2C2A   LPDO1      0.00      0.000 ! from OD2C1D   LPDO1      0.00      0.000 ! FORM
+OD2C2A    DUMH    536.50      0.970 ! from OD31A    HDP1A    536.50      0.970 ! MEOH, methanol 
+
+ANGLES
+HDP1C   CD2O2A   OD2C2A   55.500  118.000   ! from OD2C1D CD2O1C HDP1C  PENALTY  3.000
+CD2O2A   OD2C2A   DUMH   65.000  108.000   ! from CD2O3A   OD31A   HDP1A   65.000  108.000   ! from CD2R6A OD31A HDP1A  PENALTY  7.000
+
+DIHEDRALS
+HDP1C   CD2O2A   OD2C2A   DUMH   0.060  1  0.000   ! from HDA1A CD31A OD31A HDP1A  PENALTY 31.000
+HDP1C   CD2O2A   OD2C2A   DUMH   0.060  2  0.000   ! from HDA1A CD31A OD31A HDP1A  PENALTY 31.000
+HDP1C   CD2O2A   OD2C2A   DUMH   0.000  3  0.000   ! from HDA1A CD31A OD31A HDP1A  PENALTY 31.000
+DUMH   OD2C2A   CD2O2A   OD2C2A   1.110  2  180.000   ! from OD2C3A CD2O3A OD30D HDP1A  PENALTY 814.000
+
+IMPROPERS
+
+
+END
+RETURN

protex/forcefield/forh.str

@@ -0,0 +1,77 @@
+* 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.
+
+RESI  FORH      0.0000
+GROUP
+ATOM C      CD2O3A         0.380  ALPHA   -1.2613  THOLE   1.0543
+ATOM H      HDP1C          0.110 
+ATOM O2     OD2C1A         0.000  ALPHA   -0.7131  THOLE   0.5698 ! You may also consider OD2C1C  OD2C3A Equivalent Atomtypes
+ATOM O1     OD31A          0.000  ALPHA   -0.8315  THOLE   0.7494 ! You may also consider OD31C  OD31E  OD31F Equivalent Atomtypes
+ATOM HO1    HDP1A          0.400 
+ATOM LPO21  LPDO1         -0.200
+ATOM LPO22  LPDO1         -0.200
+ATOM LPO11  LPD           -0.245
+ATOM LPO12  LPD           -0.245
+
+BOND C  O1 
+BOND C  H 
+BOND C  O2 
+BOND O1  HO1 
+BOND  LPO21  O2 
+BOND  LPO22  O2 
+BOND  LPO11  O1 
+BOND  LPO12  O1 
+
+LONE RELATIVE LPO21  O2  C  O1 DIST 0.3500 ANGLE  110.00 DIHE    0.00
+LONE RELATIVE LPO22  O2  C  O1 DIST 0.3500 ANGLE  110.00 DIHE  180.00
+LONE BISECTOR LPO11  O1  C  HO1 DIST 0.3500 ANGLE  110.00 DIHE   90.00
+LONE BISECTOR LPO12  O1  C  HO1 DIST 0.3500 ANGLE  110.00 DIHE  270.00
+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   OD31A   150.000  1.330   ! from CD2O3A OD30C  PENALTY  5.000
+CD2O3A   HDP1C   310.000  1.104   ! from CD2O1C HDP1C  PENALTY  3.000
+CD2O3A   OD2C1A   623.000  1.239   ! from CD2O4A OD2C1B  PENALTY  2.000
+
+ANGLES
+OD31A   CD2O3A   HDP1C   55.500  118.000   ! from OD2C1D CD2O1C HDP1C  PENALTY 14.000
+OD31A   CD2O3A   OD2C1A   90.000  123.000   ! from OD2C3A CD2O3A OD30C  PENALTY 17.000
+HDP1C   CD2O3A   OD2C1A   55.500  118.000   ! from OD2C1C CD2O1C HDP1C  PENALTY 295.000
+CD2O3A   OD31A   HDP1A   65.000  108.000   ! from CD2R6A OD31A HDP1A  PENALTY  7.000
+
+DIHEDRALS
+HDP1C   CD2O3A   OD31A   HDP1A   0.060  1  0.000   ! from HDA1A CD31A OD31A HDP1A  PENALTY 31.000
+HDP1C   CD2O3A   OD31A   HDP1A   0.060  2  0.000   ! from HDA1A CD31A OD31A HDP1A  PENALTY 31.000
+HDP1C   CD2O3A   OD31A   HDP1A   0.000  3  0.000   ! from HDA1A CD31A OD31A HDP1A  PENALTY 31.000
+HDP1A   OD31A   CD2O3A   OD2C1A   1.110  2  180.000   ! from OD2C3A CD2O3A OD30D HDP1A  PENALTY 814.000
+
+IMPROPERS
+
+
+END
+RETURN