Re: [Apbs-users] Limiting calculations to specific residues
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Re: [Apbs-users] Limiting calculations to specific residues
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From: Nathan B. <ba...@bi...> - 2009-06-16 01:02:48
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Hi Sean -- I'm still not sure I completely understand what you're looking for; however, one possibility might be to set all of the charges in your PQR file to zero except for the residues of interest. This change should be easy to make; the PQR format is described in the APBS user guide: http://cardon.wustl.edu/MediaWiki/index.php/PQR_format Good luck! -- Nathan On Jun 15, 2009, at 8:22 AM, Sean Barron wrote: > Hello Dr. Baker, > > I want to run linearized Poisson-Boltzman calculations of > electrostatic potential mapped only to the atoms of interest. In my > *.in file, I have the "comps" flag present for the "calcEnergy" > command, but I was wondering if there was a way to limit the number > of atoms that are written to the output file. > > We have APBS installed on local machines running Linux, so I could > probably write a script that can extract the relevant information. I > was just curious if this function was supported in APBS, maybe > through the "Print" or "Write" commands? > > Thanks! > Sean > > > Nathan Baker wrote: >> >> Hi Sean -- >> >> Can you say more about what types of calculations you're thinking >> of? Are these just potential visualization calculations or more >> complicated energy calculations? >> >> Thanks, >> >> Nathan >> >> On Jun 13, 2009, at 12:58 PM, Sean Barron wrote: >> >>> Hello everyone, >>> >>> I am completely new to APBS, and I was wondering if there a way to >>> limit the electrostatic calculations to specific residues within a >>> given protein? I have introduced point mutations in silico and >>> only need data from those positions. >>> >>> Any help would be greatly appreciated. >>> >>> Cheers, >>> Sean >>> ----------- >>> Sean Barron >>> Curriculum in Neurobiology & Dept. of Pharmacology >>> University of North Carolina at Chapel Hill >>> sb...@me... >>> ------------------------------------------------------------------------------ >>> Crystal Reports - New Free Runtime and 30 Day Trial >>> Check out the new simplified licensing option that enables unlimited >>> royalty-free distribution of the report engine for externally facing >>> server and web deployment. >>> http://p.sf.net/sfu/businessobjects_______________________________________________ >>> apbs-users mailing list >>> apb...@li... >>> https://lists.sourceforge.net/lists/listinfo/apbs-users >> >> -- >> Associate Professor, Dept. of Biochemistry and Molecular Biophysics >> Director, Molecular Biophysics Graduate Program >> Center for Computational Biology, Washington University in St. Louis >> Web: http://cholla.wustl.edu/ >> >> >> >> >> >> >> >> >> >> >> -- >> Associate Professor, Dept. of Biochemistry and Molecular Biophysics >> Director, Molecular Biophysics Graduate Program >> Center for Computational Biology, Washington University in St. Louis >> Web: http://cholla.wustl.edu/ >> >> >> >> >> >> >> >> >> >> ------------------------------------------------------------------------------ >> Crystal Reports - New Free Runtime and 30 Day Trial >> Check out the new simplified licensing option that enables unlimited >> royalty-free distribution of the report engine for externally facing >> server and web deployment. >> http://p.sf.net/sfu/businessobjects >> >> _______________________________________________ >> apbs-users mailing list >> apb...@li... >> https://lists.sourceforge.net/lists/listinfo/apbs-users >> > > > > ----------- > Sean Barron > sb...@me... -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Director, Molecular Biophysics Graduate Program Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ |