Dear GMX users, I could make topology file of a ligand molecule by PRODRG but it has wrong charge on each atom and as mentioned in Gromacs tutorial (protein-ligand complex) I have used quantum mechanic calculation (like spartan) to correct its charge:
.itp file from PRODRG: [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 CH3 1 DRG CAA 1 0.092 15.0350 2 CH2 1 DRG CAI 1 0.107 14.0270 3 NL 1 DRG N 1 0.702 14.0067 4 H 1 DRG H 1 -0.007 1.0080 5 CH2 1 DRG CAJ 1 0.106 14.0270 6 CH3 1 DRG CAB 2 0.071 15.0350 7 CH2 1 DRG CA 2 0.089 14.0270 8 C 1 DRG C 2 0.343 12.0110 9 O 1 DRG O 2 -0.733 15.9994 10 N 1 DRG NAL 2 0.120 14.0067 11 H 1 DRG HKL 2 -0.009 1.0080 12 C 1 DRG CAP 2 0.119 12.0110 13 C 1 DRG CAN 3 -0.037 12.0110 14 CH3 1 DRG CAC 3 0.047 15.0350 15 CR1 1 DRG CAG 3 -0.020 12.0110 16 HC 1 DRG HAN 3 0.013 1.0080 17 CR1 1 DRG CAF 3 -0.020 12.0110 18 HC 1 DRG HAM 3 0.013 1.0080 19 CR1 1 DRG CAH 3 -0.020 12.0110 20 HC 1 DRG HAO 3 0.013 1.0080 21 C 1 DRG CAO 3 -0.036 12.0110 22 CH3 1 DRG CAD 3 0.047 15.0350 .itp file whit modification based on Hatree-Fock quantum chemical calculations using 6-31* basis set: ; nr type resnr resid atom cgnr charge mass 1 CH3 1 DRG CAA 1 -0.507 15.0350 2 CH2 1 DRG CAI 1 0.117 14.0270 3 NL 1 DRG N 1 0.372 14.0067 4 H 1 DRG H 1 0.391 1.0080 5 CH2 1 DRG CAJ 1 0.104 14.0270 6 CH3 1 DRG CAB 2 -0.512 15.0350 7 CH2 1 DRG CA 2 -0.368 14.0270 8 C 1 DRG C 2 0.983 12.0110 9 O 1 DRG O 2 -0.656 15.9994 10 N 1 DRG NAL 2 -0.689 14.0067 11 H 1 DRG HKL 2 0.391 1.0080 12 C 1 DRG CAP 2 -0.105 12.0110 13 C 1 DRG CAN 3 0.367 12.0110 14 CH3 1 DRG CAC 3 -0.700 15.0350 15 CR1 1 DRG CAG 3 -0.364 12.0110 16 HC 1 DRG HAN 3 0.189 1.0080 17 CR1 1 DRG CAF 3 -0.079 12.0110 18 HC 1 DRG HAM 3 0.159 1.0080 19 CR1 1 DRG CAH 3 -0.412 12.0110 20 HC 1 DRG HAO 3 0.202 1.0080 21 C 1 DRG CAO 3 0.425 12.0110 22 CH3 1 DRG CAD 3 -0.739 15.0350 .itp file of a reference (dynamic and structural properties of lidocaine in lipid bilayer,Carl-Johan Högberg, Arnold Maliniak, Alexander P. Lyubartsev ⁎ http://www.elsevier.com/locate/biophyschem ): [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 CH3 1 DRG CAA 1 0.025 15.0350 2 CH2 1 DRG CAI 1 0.248 14.0270 3 NL 1 DRG N 1 0.049 14.0067 4 H 1 DRG H 1 0.405 1.0080 5 CH2 1 DRG CAJ 1 0.248 14.0270 6 CH3 1 DRG CAB 2 0.025 15.0350 7 CH2 1 DRG CA 2 0.000 14.0270 8 C 1 DRG C 2 0.227 12.0110 9 O 1 DRG O 2 -0.411 15.9994 10 N 1 DRG NAL 2 0.088 14.0067 11 H 1 DRG HKL 2 0.008 1.0080 12 C 1 DRG CAP 2 0.088 12.0110 13 C 1 DRG CAN 3 -0.004 12.0110 14 CH3 1 DRG CAC 3 0.030 15.0350 15 CR1 1 DRG CAG 3 -0.013 12.0110 16 HC 1 DRG HAN 3 1.0080 17 CR1 1 DRG CAF 3 -0.013 12.0110 18 HC 1 DRG HAM 3 1.0080 19 CR1 1 DRG CAH 3 -0.013 12.0110 20 HC 1 DRG HAO 3 1.0080 21 C 1 DRG CAO 3 -0.005 12.0110 22 CH3 1 DRG CAD 3 0.022 15.0350 I have tried all of them several times but they are very different from each other. What can I do? and when I use for example spartan to calculate charges how can I select which one of methods are the best ? what is the reliable reference to compare my result with? Thanks a lot in advance.
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