[PyMOL] problems with apbs/pqr
Hi all, My apologies if this has been covered by this list before, but I couldn't find mention of it: I'm trying to calculate an electrostatic surface for my protein. The APBS Tools plug-in crashes with the message: WARNING: 502 atoms did not have formal charges assigned WARNING: 1051 atoms did not have properties assigned This happens whether I use a pqr file from PDB2PQR or the PyMol generated PQR. I'm running OS X (Intel), Pymol version 1.2r0. I also tried it though on a linux machine, and got the same error. This plug-in works fine with several other coordinate files. I tried removing the chain ids from the pdb file, but that did not help. Can anyone offer any advice on this? --James -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] problems with apbs/pqr
James, It sounds like there mayy be something other than canonical amino acids in your structure which might need to be removed prior to performing a calculation. These may be alternate conformations of amino acid side chains, ligands, or other unrecognized groups which cannot be processed for APBS. Cheers, Warren -Original Message- From: James Whittle [mailto:whit...@mit.edu] Sent: Wed 8/5/2009 5:01 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] problems with apbs/pqr Hi all, My apologies if this has been covered by this list before, but I couldn't find mention of it: I'm trying to calculate an electrostatic surface for my protein. The APBS Tools plug-in crashes with the message: WARNING: 502 atoms did not have formal charges assigned WARNING: 1051 atoms did not have properties assigned This happens whether I use a pqr file from PDB2PQR or the PyMol generated PQR. I'm running OS X (Intel), Pymol version 1.2r0. I also tried it though on a linux machine, and got the same error. This plug-in works fine with several other coordinate files. I tried removing the chain ids from the pdb file, but that did not help. Can anyone offer any advice on this? --James -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] problems with apbs/pqr
Whoops! I accidentally replied only to James, rather than to the whole list. PyMOL has some trouble with assigning charges. PDB2PQR handles it, but manages to generate a bad PQR (missing the space between some columns with leading minus signs, e.g. -100.2345-100.2345). Fixing the PQR file by hand fixes the problem. -michael On Wed, Aug 5, 2009 at 11:35 AM, Warren DeLano war...@delsci.com wrote: James, It sounds like there mayy be something other than canonical amino acids in your structure which might need to be removed prior to performing a calculation. These may be alternate conformations of amino acid side chains, ligands, or other unrecognized groups which cannot be processed for APBS. Cheers, Warren -Original Message- From: James Whittle [mailto:whit...@mit.edu whit...@mit.edu] Sent: Wed 8/5/2009 5:01 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] problems with apbs/pqr Hi all, My apologies if this has been covered by this list before, but I couldn't find mention of it: I'm trying to calculate an electrostatic surface for my protein. The APBS Tools plug-in crashes with the message: WARNING: 502 atoms did not have formal charges assigned WARNING: 1051 atoms did not have properties assigned This happens whether I use a pqr file from PDB2PQR or the PyMol generated PQR. I'm running OS X (Intel), Pymol version 1.2r0. I also tried it though on a linux machine, and got the same error. This plug-in works fine with several other coordinate files. I tried removing the chain ids from the pdb file, but that did not help. Can anyone offer any advice on this? --James -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS) -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] problems with apbs/pqr
Thanks, Michael. One further note- this problem can occur even with only a standard protein (no alternate conformations, ligands, etc.). The solution is simple: just replace all '-' characters with ' -'. --James On Aug 5, 2009, at 12:23 PM, Michael Lerner wrote: Whoops! I accidentally replied only to James, rather than to the whole list. PyMOL has some trouble with assigning charges. PDB2PQR handles it, but manages to generate a bad PQR (missing the space between some columns with leading minus signs, e.g. -100.2345-100.2345). Fixing the PQR file by hand fixes the problem. -michael On Wed, Aug 5, 2009 at 11:35 AM, Warren DeLano war...@delsci.com wrote: James, It sounds like there mayy be something other than canonical amino acids in your structure which might need to be removed prior to performing a calculation. These may be alternate conformations of amino acid side chains, ligands, or other unrecognized groups which cannot be processed for APBS. Cheers, Warren -Original Message- From: James Whittle [mailto:whit...@mit.edu] Sent: Wed 8/5/2009 5:01 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] problems with apbs/pqr Hi all, My apologies if this has been covered by this list before, but I couldn't find mention of it: I'm trying to calculate an electrostatic surface for my protein. The APBS Tools plug-in crashes with the message: WARNING: 502 atoms did not have formal charges assigned WARNING: 1051 atoms did not have properties assigned This happens whether I use a pqr file from PDB2PQR or the PyMol generated PQR. I'm running OS X (Intel), Pymol version 1.2r0. I also tried it though on a linux machine, and got the same error. This plug-in works fine with several other coordinate files. I tried removing the chain ids from the pdb file, but that did not help. Can anyone offer any advice on this? --James -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol- us...@lists.sourceforge.net -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol- us...@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS) -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
