Re: [AMBER] Using PQR files produced by PDB2PQR as input for tleap/xleap

From: David A. Case <>
Date: Thu, 9 Jun 2011 06:32:34 -0400

On Thu, Jun 09, 2011, Azat Mukhametov wrote:

> Yes, it looks that something is wrong with data in PQR file (see below):
> ATOM 1 N GLY A 43 15.790 10.898 22.016 0.2943 1.8240

These lines are all wrong: they have the residue name in columns 19-21,
whereas they should be in columns 18-20. And everything else on the line
is one column too far to the right. You could fix this by removing the space
before each residue name.

You might contact the people who wrote PDB2PQR to see if they have comments
or ideas. (Another alternative is to use the H++ server to assign protonation
states.) Maybe the PDB2PQR people have a different idea of what should be
in a PQR file than we do (after all, it's not a standard), but adding an extra
space to an otherwise useful pdb-like format doesn't seem to make much sense
(to me, anyway).


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Received on Thu Jun 09 2011 - 04:00:03 PDT
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