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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Washington University School of Medicine
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