From: Warren D. <wa...@de...> - 2009-08-05 15:38:37
|
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:whittle@MIT.EDU] Sent: Wed 8/5/2009 5:01 AM To: pym...@li... 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 (PyM...@li...) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pym...@li... |
From: Michael L. <mgl...@gm...> - 2009-08-05 16:24:00
|
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 <wa...@de...> 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:whittle@MIT.EDU <whittle@MIT.EDU>] > Sent: Wed 8/5/2009 5:01 AM > To: pym...@li... > 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > > > > > > > > ------------------------------------------------------------------------------ > 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- 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) |
From: James W. <whittle@MIT.EDU> - 2009-08-05 16:31:50
|
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 <wa...@de...> > 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:whittle@MIT.EDU] > Sent: Wed 8/5/2009 5:01 AM > To: pym...@li... > 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol- > us...@li... > > > > > > > > ------------------------------------------------------------------------------ > 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol- > us...@li... > > > > -- > 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) |