PQR files make from pdb2pqr are different to GROMACS
I have a pdb file and I would like to make a pqr one. In GROMACS, I use editconf -mead to produce the pqr file, with topol.top taken from pdb2gmx and use it to produce pdb file, then use pdb2pqr. Which one is the better?
First 10 lines of PQR made from GROMACS
ATOM 1 N PRO A 1 0.63000 39.63000 17.25000 -<PHONE_NUMBER>
ATOM 2 H1 PRO A 1 1.37000 39.93000 17.89000 0.3120 0.5345
ATOM 3 H2 PRO A 1 0.24000 40.48000 <PHONE_NUMBER> 0.3120 0.5345
ATOM 4 CD PRO A 1 1.21000 38.79000 16.18000 -0.0120 <PHONE_NUMBER>
ATOM 5 HD1 PRO A 1 2.30000 38.76000 16.29000 0.1000 0.9800
ATOM 6 HD2 PRO A 1 0.96000 39.21000 15.20000 0.1000 0.9800
ATOM 7 CG PRO A 1 0.63000 37.39000 16.30000 -0.1210 <PHONE_NUMBER>
ATOM 8 HG1 PRO A 1 1.28000 36.80000 <PHONE_NUMBER> 0.1000 1.3248
ATOM 9 HG2 PRO A 1 0.52000 36.90000 15.<PHONE_NUMBER>.1000 1.3248
ATOM 10 CB PRO A 1 -0.72000 37.64000 <PHONE_NUMBER> -0.1150 <PHONE_NUMBER>
First 10 lines of PQR made from pqd2pqr:
ATOM 1 N PRO 1 <PHONE_NUMBER> -<PHONE_NUMBER>
ATOM 2 H PRO 1 1.370 39.930 17.890 0.3120 0.6000
ATOM 3 H2 PRO 1 0.240 40.480 <PHONE_NUMBER> 0.3120 0.6000
ATOM 4 CD PRO 1 1.210 38.790 16.180 -0.0120 1.9080
ATOM 5 HD3 PRO 1 2.300 38.760 16.290 0.1000 1.1000
ATOM 6 HD2 PRO 1 0.960 39.210 15.200 0.1000 1.1000
ATOM 7 CG PRO 1 <PHONE_NUMBER> -0.1210 1.9080
ATOM 8 HG3 PRO 1 1.280 36.800 <PHONE_NUMBER> 0.1000 1.4870
ATOM 9 HG2 PRO 1 0.520 36.900 15.330 0.1000 1.4870
ATOM 10 CB PRO 1 -<PHONE_NUMBER> -0.1150 1.9080
These are from 3B7V, a HIV-1 protease. It has been minimized energy. 268