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

From: Jason Swails <>
Date: Thu, 9 Jun 2011 10:47:10 -0600

On Thu, Jun 9, 2011 at 4:32 AM, David A. Case <>wrote:

> 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.

If I recall correctly, the PDB2PQR manual/description states that it is
*loosely* based on the PDB format. Where PDB assigns specific meanings to
columns (giving it a fixed format), the PQR file format's important features
are whitespace delimiters (making it free format). Thus, I'm not surprised
that PQRs aren't read by the loadpdb command in leap (and probably explains
why the column width is off compared to what loadpdb expects). I would
suggest against using PQRs for leap, since it appears to follow the PDB
format more strictly than the PQR format does.


(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).
> ....dac
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> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Thu Jun 09 2011 - 10:00:02 PDT
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