1
$\begingroup$

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 -0.2020  1.6250      
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  16.88000  0.3120  0.5345      
ATOM  4 CD   PRO A   1     1.21000  38.79000  16.18000 -0.0120  1.6998      
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  1.6998      
ATOM  8 HG1  PRO A   1     1.28000  36.80000  16.95000  0.1000  1.3248      
ATOM  9 HG2  PRO A   1     0.52000  36.90000  15.33000  0.1000  1.3248      
ATOM  10 CB  PRO A   1    -0.72000  37.64000  16.99000 -0.1150  1.6998      

First 10 lines of PQR made from pqd2pqr:

ATOM      1  N   PRO     1       0.630  39.630  17.250 -0.2020 1.8240
ATOM      2  H   PRO     1       1.370  39.930  17.890  0.3120 0.6000
ATOM      3  H2  PRO     1       0.240  40.480  16.880  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       0.630  37.390  16.300 -0.1210 1.9080
ATOM      8  HG3 PRO     1       1.280  36.800  16.950  0.1000 1.4870
ATOM      9  HG2 PRO     1       0.520  36.900  15.330  0.1000 1.4870
ATOM     10  CB  PRO     1      -0.720  37.640  16.990 -0.1150 1.9080

These are from 3B7V, a HIV-1 protease. It has been minimized energy.

$\endgroup$
3
$\begingroup$

The Van der Walls radius - last column in the output - is calculated from the force field. Probably pdb2pqr and editconf uses different force fields, hence different radius. I don't use pdb2pqr, but it seems (1) AMBER99 is the default force field, though CHARMM, PARSE and TYL06 are supported. Gromacs' editconf reads force field from topology file generated by pdb2gmx (2). In my system pdb2gmx defaults to AMBER03. Try

pdb2gmx -ff select

Which one is better depends on your problem. Are you generating input to APBS? If so, I would use pdb2pqr.

Ref:

(1) http://www.poissonboltzmann.org/pdb2pqr/user-guide/using-pdb2pqr

(2) http://manual.gromacs.org/online/pdb2gmx.html

$\endgroup$
  • $\begingroup$ Yes, I use to generate input to APBS. I forgot to tell that I use AMBER99 for both cases. I will use pdb2pqr then. Thank you so much. $\endgroup$ – Ooker May 22 '14 at 18:33

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.