I have also been unable to use pdb2pqr within the
plugin (I had similar problems althought I was only
using standard residues), but what I did is to use
pqr2pdb as stand-alone
program and then feed the plugin with the previously
generated pqr files.
Hope it helps
> Message: 2
> Date: Wed, 22 Nov 2006 09:27:50 +0100
> From: Florian Schmitzberger
> Subject: [PyMOL] apbs plugin in pymol
> To: pymol-users@...
> Content-Type: text/plain; charset="us-ascii"
> Dear All,
> I am having a small problem using the apbs plugin in
> pymol on my pdb
> (I am using fink installed pymol and apbs versions
> on Mac OSX 10.4.8).
> When I try to run apbs I received the following
> "Unable to assign parameters for 100 atoms in the
> unassigned. Please either remove these unassigned
> atoms and re-
> start ..."
> In principle, I think I understand the problem is
> that pdb2pqr cannot
> assign charges to certain atoms, in my case
> modified cysteine residues.
> My question would be what the best way to fare with
> those atoms is.
> Since the modification introduces an acidic patch,
> if possible I
> would like to leave the atoms in (rather than remove
> them) when
> calculating surface charge representation, as this
> could be informative.
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