Re: [Apbs-users] Error parsing atom in binary package
Biomolecular electrostatics software
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From: Nathan B. <ba...@bi...> - 2009-07-03 11:40:11
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Hello -- As Michael pointed out, it appears the columns of the PQR file have run together (e.g., around line 24433). If you process this structure through PDB2PQR (http://pdb2pqr.sf.net/), it should fix the problem. -- Nathan On Jul 2, 2009, at 9:28 PM, Tran Duc Trinh wrote: > Hello, > Thanks for your response. I attach my molecule here for your > reference. I noticed that if i cut back the number of atoms under > 20,000 then there is no problem with the parsing error. The molecule > is the model of actin filament with 13 subunit. Therefore the total > of atom is about 75,500 atoms > I am interest to have the electrostatic potential around my molecule > to subsequently carry the Brownian Dynamic simulation of the > filament interaction. > If the binary package couldn't accomodate the molecule, can you > direct me to any source that can get the problem solved. > Best regards, > Trinh > > > > > +++++++++++++++++++ > > Life may be hard on you. > Do not blame anyone but try your best. > > > --- On Thu, 7/2/09, Yong Huang <yhu...@gm...> wrote: > > From: Yong Huang <yhu...@gm...> > Subject: Re: Error parsing atom in binary package > To: "Tran Duc Trinh" <tra...@ya...> > Cc: apb...@li... > Date: Thursday, July 2, 2009, 7:30 PM > > Hello, > > Can you send us a copy of the pdb (or pqr) that you have problem > with? It really helps if you could give us an example. > > Thanks, > > Yong > > > On Thu, Jul 2, 2009 at 5:58 PM, Tran Duc Trinh > <tra...@ya...> wrote: > I am new to apbs and currently using the binary package for Windows > on my desktop. It works very good for small molecule, however it > reported problem "Error parsing atom #" for bigger problem. > I think that my be because of the limitation in the number of atoms > of the binary package for Windows. Can anyone tells me what is the > maximum number of atoms for binary package? My macromolecule has > more than 50000 atoms. Any help to overcome the problem is very > appreciated. > Thanks, > Trinh > > > > > +++++++++++++++++++ > > Life may be hard on you. > Do not blame anyone but try your best. > > > -- > Yong Huang, D.Sc. > > Center for Computational Biology > Washington University School of Medicine > > <Actin_13units.pqr> -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Director, Computational and Molecular Biophysics Graduate Program Center for Computational Biology, Washington University in St. Louis Web: http://bakergroup.wustl.edu/ |