Hi Florian 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 Raul > Message: 2 > Date: Wed, 22 Nov 2006 09:27:50 +0100 > From: Florian Schmitzberger > <florian.schmitzber...@ki.se> > Subject: [PyMOL] apbs plugin in pymol > To: pymol-users@lists.sourceforge.net > Message-ID: > <e292b572-a3fe-4dd9-8557-52bc44e10...@ki.se> > 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 > message: > > "Unable to assign parameters for 100 atoms in the > selection > 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 > posttranslationally > 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. __________________________________________________ Correo Yahoo! Espacio para todos tus mensajes, antivirus y antispam ¡gratis! Regístrate ya - http://correo.espanol.yahoo.com/
