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

From: David A. Case <>
Date: Thu, 9 Jun 2011 04:36:55 -0400

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

> I use another computer for calculations, just checked:
> I used:
> prot = loadpdb prot.pqr
> It gives huge number of warnings and mistakes

Can you look carefully at the first few error messages, and/or post the
beginning of your pqr file? A wild guess is that PDB2PQR is putting out an
odd format, not really compatible with pdb, or perhaps with the Amber

I'm not sure I understand the original problem: why not use the pdb file that
you used for input to PDB2PQR? Or is there some other reason you have a pqr
format file, but not a pdb format file?


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Received on Thu Jun 09 2011 - 02:00:03 PDT
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