Hello, I first used Antechamber and Leap to generate the topology and coordinate files for benzamide.pdb.
I then converted them to gromacs formats and added the water molecules using the following commands: editconf -f benz.gro -bt dodecahedron -d 1.2 -o benz_box.gro genbox -cp benz_box.gro -cs tip4p.gro (there was no tip3p.gro) -p benz.top -o benz_solvated.gro ************************************************************* ; benz.top created by rdparm2gmx.pl Wed Jun 8 14:58:07 MDT 2011 [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon n n 0.0000 0.0000 A 3.25000e-01 7.11280e-01 c c 0.0000 0.0000 A 3.39967e-01 3.59824e-01 ha ha 0.0000 0.0000 A 2.59964e-01 6.27600e-02 hn hn 0.0000 0.0000 A 1.06908e-01 6.56888e-02 ca ca 0.0000 0.0000 A 3.39967e-01 3.59824e-01 o o 0.0000 0.0000 A 2.95992e-01 8.78640e-01 [ moleculetype ] ; Name nrexcl solute 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB 1 ca 1 MOL C 1 -0.07700 12.000000 2 ca 1 MOL C1 2 -0.13800 12.000000 3 ca 1 MOL C2 3 -0.10900 12.000000 4 ca 1 MOL C3 4 -0.13900 12.000000 5 ca 1 MOL C4 5 -0.10500 12.000000 6 ca 1 MOL C5 6 -0.14160 12.000000 7 c 1 MOL C6 7 0.67070 12.000000 8 o 1 MOL O 8 -0.61010 16.000000 9 n 1 MOL N 9 -0.67400 14.000000 10 ha 1 MOL H 10 0.15600 1.000000 11 ha 1 MOL H1 11 0.13800 1.000000 12 ha 1 MOL H2 12 0.13500 1.000000 13 ha 1 MOL H3 13 0.13600 1.000000 14 ha 1 MOL H4 14 0.13300 1.000000 15 hn 1 MOL H5 15 0.31750 1.000000 16 hn 1 MOL H6 16 0.30750 1.000000 [ bonds ] ; ai aj funct r k 1 10 1 1.0870e-01 2.8811e+05 2 11 1 1.0870e-01 2.8811e+05 3 12 1 1.0870e-01 2.8811e+05 4 13 1 1.0870e-01 2.8811e+05 5 14 1 1.0870e-01 2.8811e+05 9 15 1 1.0090e-01 3.4326e+05 9 16 1 1.0090e-01 3.4326e+05 1 2 1 1.3870e-01 4.0033e+05 1 6 1 1.3870e-01 4.0033e+05 2 3 1 1.3870e-01 4.0033e+05 3 4 1 1.3870e-01 4.0033e+05 4 5 1 1.3870e-01 4.0033e+05 5 6 1 1.3870e-01 4.0033e+05 6 7 1 1.4870e-01 2.9263e+05 7 8 1 1.2140e-01 5.4225e+05 7 9 1 1.3450e-01 4.0016e+05 [ pairs ] ; ai aj funct 1 12 1 1 14 1 2 13 1 10 3 1 3 14 1 4 11 1 5 12 1 10 5 1 6 11 1 6 13 1 6 15 1 6 16 1 10 7 1 7 14 1 8 15 1 8 16 1 10 11 1 11 12 1 12 13 1 13 14 1 1 4 1 1 8 1 1 9 1 2 5 1 2 7 1 6 3 1 4 7 1 5 8 1 5 9 1 [ angles ] ; ai aj ak funct theta cth 1 2 11 1 1.2001e+02 4.0551e+02 2 1 10 1 1.2001e+02 4.0551e+02 2 3 12 1 1.2001e+02 4.0551e+02 3 2 11 1 1.2001e+02 4.0551e+02 3 4 13 1 1.2001e+02 4.0551e+02 4 3 12 1 1.2001e+02 4.0551e+02 4 5 14 1 1.2001e+02 4.0551e+02 5 4 13 1 1.2001e+02 4.0551e+02 6 1 10 1 1.2001e+02 4.0551e+02 6 5 14 1 1.2001e+02 4.0551e+02 7 9 15 1 1.1846e+02 4.1179e+02 7 9 16 1 1.1846e+02 4.1179e+02 15 9 16 1 1.1785e+02 3.3246e+02 1 2 3 1 1.1997e+02 5.6216e+02 1 6 5 1 1.1997e+02 5.6216e+02 1 6 7 1 1.2014e+02 5.4091e+02 2 1 6 1 1.1997e+02 5.6216e+02 2 3 4 1 1.1997e+02 5.6216e+02 3 4 5 1 1.1997e+02 5.6216e+02 4 5 6 1 1.1997e+02 5.6216e+02 5 6 7 1 1.2014e+02 5.4091e+02 6 7 8 1 1.2344e+02 5.7463e+02 6 7 9 1 1.1514e+02 5.7296e+02 8 7 9 1 1.2203e+02 6.3455e+02 [ dihedrals ] ;i j k l func C0 ... C5 1 2 3 12 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; 1 6 5 14 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; 2 3 4 13 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; 10 1 2 3 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; 3 4 5 14 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; 4 3 2 11 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; 5 4 3 12 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; 10 1 6 5 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; 6 1 2 11 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; 6 5 4 13 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; 6 7 9 15 3 20.92000 0.00000 -20.92000 0.00000 0.00000 0.00000 ; 6 7 9 16 3 20.92000 0.00000 -20.92000 0.00000 0.00000 0.00000 ; 10 1 6 7 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; 7 6 5 14 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; 8 7 9 15 3 29.28800 -8.36800 -20.92000 0.00000 0.00000 0.00000 ; 8 7 9 16 3 29.28800 -8.36800 -20.92000 0.00000 0.00000 0.00000 ; 10 1 2 11 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; 11 2 3 12 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; 12 3 4 13 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; 13 4 5 14 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; 10 1 6 2 3 9.20480 0.00000 -9.20480 0.00000 0.00000 0.00000 ; 1 3 2 11 3 9.20480 0.00000 -9.20480 0.00000 0.00000 0.00000 ; 2 4 3 12 3 9.20480 0.00000 -9.20480 0.00000 0.00000 0.00000 ; 3 5 4 13 3 9.20480 0.00000 -9.20480 0.00000 0.00000 0.00000 ; 4 6 5 14 3 9.20480 0.00000 -9.20480 0.00000 0.00000 0.00000 ; 7 15 9 16 3 9.20480 0.00000 -9.20480 0.00000 0.00000 0.00000 ; 1 2 3 4 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; 1 6 5 4 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; 1 6 7 8 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; 1 6 7 9 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; 2 1 6 5 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; 2 1 6 7 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; 2 3 4 5 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; 6 1 2 3 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; 3 4 5 6 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; 4 5 6 7 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; 5 6 7 8 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; 5 6 7 9 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; 6 9 7 8 3 87.86400 0.00000 -87.86400 0.00000 0.00000 0.00000 ; [ system ] 16 system in water [ molecules ] ; Compound nmols solute 1 SOL 697 ******************************************************************************************* When I try to run the minimizer, I get this error: Fatal error: No such moleculetype SOL **************************************************************** I added this line to benz.top file: *#include "amber99.ff/tip4p.itp"* [ system ] 16 system in water I get this error when minimizing: Fatal error: Atomtype OW_tip4p not found Thanks Massih
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