Thread: Re: [Apbs-users] question about unassigned atoms
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From: Haiming C. <hc...@hs...> - 2008-09-28 03:31:01
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I am new to Pymol and have been trying to show electrostatic potential of a protein. I always got an error like “Unable to assign parameters for the x atoms in selection ‘unassigned’. Please either remove these unassigned atoms and re-start the calculation or fix their parameters in the generated PQR file and run the calculation using the modified PQR file”. Any advice to resolve this? A bit more details, I worked on a Windows XP and the default folder for pqr file is My Documents. Thank you in advance. Haiming |
From: Haiming C. <hc...@hs...> - 2008-10-08 02:32:21
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Thank you very much for addressing my question. I managed to get it work but got another naive question. Can you possibly mutate a residue and examine the change on eletrostatic potential by APBS? Warmest regards, Haiming >>> Nathan Baker <nat...@ma...> 10/04/08 9:20 PM >>> Hello -- Have you tried out the tutorial at http://apbs.sourceforge.net/doc/tutorial/index.html#pymol-sect for this type of visualization? You might try using PDB2PQR to generate your input PQR file. Also, please check this list for various warnings about running APBS calculations under Windows in paths with spaces in the pathname. Thanks, Nathan On Sep 27, 2008, at 10:18 PM, Haiming Cao wrote: > I am new to Pymol and have been trying to show electrostatic > potential of a protein. I always got an error like “Unable to > assign parameters for the x atoms in selection ‘unassigned’. Please > either remove these unassigned atoms and re-start the calculation or > fix their parameters in the generated PQR file and run the > calculation using the modified PQR file”. Any advice to resolve > this? A bit more details, I worked on a Windows XP and the default > folder for pqr file is My Documents. > > Thank you in advance. > > Haiming > > > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win > great prizes > Grand prize is a trip for two to an Open Source event anywhere in > the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ |
From: Nathan B. <nat...@ma...> - 2008-10-09 00:17:52
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Hello -- > Thank you very much for addressing my question. I managed to get it > work but got another naive question. Can you possibly mutate a > residue and examine the change on eletrostatic potential by APBS? You could do this with only APBS and PDB2PQR but it's probably better to use a modeling program. It's my understanding that both PyMOL (http://pymolwiki.org/index.php/Mutagenesis ) and VMD (http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/2018.html ) -- and both of these programs interface with APBS. Use of those programs, or a different modeling package (WHATIF has a web interface for this), is probably the most straightforward option. Thanks, Nathan > > Warmest regards, > Haiming > > >>>> Nathan Baker <nat...@ma...> 10/04/08 9:20 PM >>> > Hello -- > > Have you tried out the tutorial at http://apbs.sourceforge.net/doc/tutorial/index.html#pymol-sect > for this type of visualization? You might try using PDB2PQR to > generate your input PQR file. > > Also, please check this list for various warnings about running APBS > calculations under Windows in paths with spaces in the pathname. > > Thanks, > > Nathan > > On Sep 27, 2008, at 10:18 PM, Haiming Cao wrote: > >> I am new to Pymol and have been trying to show electrostatic >> potential of a protein. I always got an error like “Unable to >> assign parameters for the x atoms in selection ‘unassigned’. Please >> either remove these unassigned atoms and re-start the calculation or >> fix their parameters in the generated PQR file and run the >> calculation using the modified PQR file”. Any advice to resolve >> this? A bit more details, I worked on a Windows XP and the default >> folder for pqr file is My Documents. >> >> Thank you in advance. >> >> Haiming >> >> >> >> ------------------------------------------------------------------------- >> This SF.Net email is sponsored by the Moblin Your Move Developer's >> challenge >> Build the coolest Linux based applications with Moblin SDK & win >> great prizes >> Grand prize is a trip for two to an Open Source event anywhere in >> the world >> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> _______________________________________________ >> apbs-users mailing list >> apb...@li... >> https://lists.sourceforge.net/lists/listinfo/apbs-users > > -- > Associate Professor, Dept. of Biochemistry and Molecular Biophysics > Center for Computational Biology, Washington University in St. Louis > Web: http://cholla.wustl.edu/ > > > > > > > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win > great prizes > Grand prize is a trip for two to an Open Source event anywhere in > the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ |
From: Nathan B. <nat...@ma...> - 2008-10-05 01:22:07
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Hello -- Have you tried out the tutorial at http://apbs.sourceforge.net/doc/tutorial/index.html#pymol-sect for this type of visualization? You might try using PDB2PQR to generate your input PQR file. Also, please check this list for various warnings about running APBS calculations under Windows in paths with spaces in the pathname. Thanks, Nathan On Sep 27, 2008, at 10:18 PM, Haiming Cao wrote: > I am new to Pymol and have been trying to show electrostatic > potential of a protein. I always got an error like “Unable to > assign parameters for the x atoms in selection ‘unassigned’. Please > either remove these unassigned atoms and re-start the calculation or > fix their parameters in the generated PQR file and run the > calculation using the modified PQR file”. Any advice to resolve > this? A bit more details, I worked on a Windows XP and the default > folder for pqr file is My Documents. > > Thank you in advance. > > Haiming > > > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win > great prizes > Grand prize is a trip for two to an Open Source event anywhere in > the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ |