Re: [ccp4bb] apbs parse error

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: apbs parse error
From: Sebastiano Pasqualato sebastiano {- dot -} pasqualato {- at -} IFOM-IEO-CAMPUS {- dot -} IT
Date: 2007-06-25

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Subject: Re: apbs parse error
From: David Gohara sdg0919 {- at -} GMAIL {- dot -} COM
Date: 2007-06-25

Hi Sebastiano,

Can you send me the problematic PDB (offlist) and we'll take a look?

Thanks,

Dave

On Jun 25, 2007, at 8:50 AM, Sebastiano Pasqualato wrote:

>
> Hi all,
> despite using the latest version of pdb2pqr ( http://
> agave.wustl.edu/pdb2pqr/server.html) and having downloaded the
> latest version of the apbs plugin for pymol, I still do not manage
> having it work with all the pdbs, most of the time getting an error
> while using the apbs plugin inparsing the pqr file:
>
> Valist_readPQR: Error parsing atom 2235!
> Error reading molecules!
>
> Interestingly, while a pdb works, if you just move it to another
> place (e.g by superposing it to another structure) and then
> recalculate the pqr file, this time the new pqr will give the
> parsing error!
>
> Does anyone know what is the problem here, or else how to calculate
> an electrostatic potential map (to be open in pymol) with another
> program?
> (I know I can switch to ccp4mg, and that's most likely what I'll
> do...)
> thanks in advance,
> ciao
> s
>
> --
> Sebastiano Pasqualato, PhD
> IFOM-IEO Campus
> Dipartimento di Oncologia Sperimentale
> Istituto Europeo di Oncologia
> via Adamello, 16
> 20139 Milano
> Italy
>
> tel +39 02 9437 5094
> fax +39 02 574 303 310
>
>
>
>
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David W. Gohara, Ph.D.
Center for Computational Biology
Washington University School of Medicine
http://www.macresearch.org
http://gohara.wustl.edu
314-362-1583 (phone)
617-216-8616 (cell)

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: apbs parse error
From: Sebastiano Pasqualato sebastiano {- dot -} pasqualato {- at -} IFOM-IEO-CAMPUS {- dot -} IT
Date: 2007-06-25

Next message:
Subject: Re: Fedora core 6 install problem
From: Flip Hoedemaeker flip {- at -} KEYDP {- dot -} COM
Date: 2007-06-25