Dear GMX users,<br><br>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:<br>
<br>.itp file from PRODRG:<br><br>[ atoms ]<br>; nr type resnr resid atom cgnr charge mass<br> 1 CH3 1 DRG CAA 1 0.092 15.0350 <br> 2 CH2 1 DRG CAI 1 0.107 14.0270 <br>
3 NL 1 DRG N 1 0.702 14.0067 <br> 4 H 1 DRG H 1 -0.007 1.0080 <br> 5 CH2 1 DRG CAJ 1 0.106 14.0270 <br> 6 CH3 1 DRG CAB 2 0.071 15.0350 <br>
7 CH2 1 DRG CA 2 0.089 14.0270 <br> 8 C 1 DRG C 2 0.343 12.0110 <br> 9 O 1 DRG O 2 -0.733 15.9994 <br> 10 N 1 DRG NAL 2 0.120 14.0067 <br>
11 H 1 DRG HKL 2 -0.009 1.0080 <br> 12 C 1 DRG CAP 2 0.119 12.0110 <br> 13 C 1 DRG CAN 3 -0.037 12.0110 <br> 14 CH3 1 DRG CAC 3 0.047 15.0350 <br>
15 CR1 1 DRG CAG 3 -0.020 12.0110 <br> 16 HC 1 DRG HAN 3 0.013 1.0080 <br> 17 CR1 1 DRG CAF 3 -0.020 12.0110 <br> 18 HC 1 DRG HAM 3 0.013 1.0080 <br>
19 CR1 1 DRG CAH 3 -0.020 12.0110 <br> 20 HC 1 DRG HAO 3 0.013 1.0080 <br> 21 C 1 DRG CAO 3 -0.036 12.0110 <br> 22 CH3 1 DRG CAD 3 0.047 15.0350 <br>
<br><br><br><br>.itp file whit modification based on Hatree-Fock quantum chemical calculations using 6-31* basis set:<br><br><br>; nr type resnr resid atom cgnr charge mass<br>
1 CH3 1 DRG CAA 1 -0.507 15.0350 <br>
2 CH2 1 DRG CAI 1 0.117 14.0270 <br>
3 NL 1 DRG N 1 0.372 14.0067 <br>
4 H 1 DRG H 1 0.391 1.0080 <br>
5 CH2 1 DRG CAJ 1 0.104 14.0270 <br>
6 CH3 1 DRG CAB 2 -0.512 15.0350 <br>
7 CH2 1 DRG CA 2 -0.368 14.0270 <br>
8 C 1 DRG C 2 0.983 12.0110 <br>
9 O 1 DRG O 2 -0.656 15.9994 <br>
10 N 1 DRG NAL 2 -0.689 14.0067 <br>
11 H 1 DRG HKL 2 0.391 1.0080 <br>
12 C 1 DRG CAP 2 -0.105 12.0110 <br>
13 C 1 DRG CAN 3 0.367 12.0110 <br>
14 CH3 1 DRG CAC 3 -0.700 15.0350 <br>
15 CR1 1 DRG CAG 3 -0.364 12.0110 <br>
16 HC 1 DRG HAN 3 0.189 1.0080 <br>
17 CR1 1 DRG CAF 3 -0.079 12.0110 <br>
18 HC 1 DRG HAM 3 0.159 1.0080 <br>
19 CR1 1 DRG CAH 3 -0.412 12.0110 <br>
20 HC 1 DRG HAO 3 0.202 1.0080 <br>
21 C 1 DRG CAO 3 0.425 12.0110 <br>
22 CH3 1 DRG CAD 3 -0.739 15.0350 <br>
<br><br><br>.itp file of a reference (dynamic and structural properties of lidocaine in lipid bilayer,Carl-Johan Högberg, Arnold Maliniak, Alexander P. Lyubartsev ⁎ <a href="http://www.elsevier.com/locate/biophyschem">http://www.elsevier.com/locate/biophyschem</a> ):<br>
<br>[ atoms ]<br>; nr type resnr resid atom cgnr charge mass<br> 1 CH3 1 DRG CAA 1 0.025 15.0350 <br> 2 CH2 1 DRG CAI 1 0.248 14.0270 <br> 3 NL 1 DRG N 1 0.049 14.0067 <br>
4 H 1 DRG H 1 0.405 1.0080 <br> 5 CH2 1 DRG CAJ 1 0.248 14.0270 <br> 6 CH3 1 DRG CAB 2 0.025 15.0350 <br> 7 CH2 1 DRG CA 2 0.000 14.0270 <br>
8 C 1 DRG C 2 0.227 12.0110 <br> 9 O 1 DRG O 2 -0.411 15.9994 <br> 10 N 1 DRG NAL 2 0.088 14.0067 <br> 11 H 1 DRG HKL 2 0.008 1.0080 <br>
12 C 1 DRG CAP 2 0.088 12.0110 <br> 13 C 1 DRG CAN 3 -0.004 12.0110 <br> 14 CH3 1 DRG CAC 3 0.030 15.0350 <br> 15 CR1 1 DRG CAG 3 -0.013 12.0110 <br>
16 HC 1 DRG HAN 3 1.0080 <br> 17 CR1 1 DRG CAF 3 -0.013 12.0110 <br> 18 HC 1 DRG HAM 3 1.0080 <br> 19 CR1 1 DRG CAH 3 -0.013 12.0110 <br>
20 HC 1 DRG HAO 3 1.0080 <br> 21 C 1 DRG CAO 3 -0.005 12.0110 <br> 22 CH3 1 DRG CAD 3 0.022 15.0350 <br><br>I have tried all of them several times but they are very different from each other.<br>
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?<br><br>Thanks a lot in advance.<br><br>
<br><br><br><br>