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I have a pdb file and I would like to make a pqr one. In GROMACS, I use editconf -mead to produce pqr, with topol.top taken from pdb2gmx or 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

Thank you so much.

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put on hold as unclear what you're asking by WYSIWYG, Chris, Cornelius, MattDMo, Chris Stronks 23 hours ago

Please clarify your specific problem or add additional details to highlight exactly what you need. As it's currently written, it’s hard to tell exactly what you're asking. See the How to Ask page for help clarifying this question.If this question can be reworded to fit the rules in the help center, please edit the question.

    
This question appears to be off-topic because it is about programming –  Chris Stronks 23 hours ago
    
This question was asked since I was new to SE, so I didn't know where to ask. Why didn't you close it at that time? –  Ooker 23 hours ago
    
It definitely has overlap with Biology and is potentially suitable. Old questions are often reviewed again later to have a look as to why they are not answered. The chance of this question being answered after all this time is slim at best. –  Chris Stronks 23 hours ago
    
Anyway, I made a cross-site duplicate here. As I said, this question was asked when I was new to SE, so I may did somethings unacceptable. Sorry about that. –  Ooker 14 hours ago
    
That's great. I hope you have had better luck elsewhere. And don't worry about it! Happens to the best of us :) –  Chris Stronks 12 hours ago