Thread: [Apbs-users] About APOLAR and MD question
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From: willting <wil...@16...> - 2007-12-28 08:49:06
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Hi, I want to calculate the binding energy between a protein and a ligand(in one complex) using apbs-0.5.1 ,and I have 2 questions. First, I downloaded the pdb file of the complex from RCSB Protein Data Bank. Except for EM,do I need to do MD for the complex(or the protein and ligand separately)before using APBS? The second question is about the APOLAR solvation energy.When I used the SASA-only Model, I set the gamma value 58.18(cal .rnol-1A-2), I noticed that the equation and the literature("Assessing implicit models...") provided by APBS 0.5.1 User Guide.When I want to used the SPT model ,how to set the gamma value ? Thanks, will |
From: Nathan B. <ba...@cc...> - 2007-12-29 16:48:44
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Hello -- > I want to calculate the binding energy between a protein and a > ligand(in one complex) using apbs-0.5.1 ,and I have 2 questions. > First, I downloaded the pdb file of the complex from RCSB Protein > Data Bank. Except for EM,do I need to do MD for the complex(or the > protein and ligand separately)before using APBS? No, not necessarily. However, this is definitely application-dependent. > > The second question is about the APOLAR solvation energy.When I > used the SASA-only Model, I set the gamma value > 58.18(cal .rnol-1A-2), I noticed that the equation and the > literature("Assessing implicit models...") provided by APBS 0.5.1 > User Guide.When I want to used the SPT model ,how to set the gamma > value ? All of these settings are made in the APOLAR block (http://apbs.sourceforge.net/doc/user-guide/index.html#apolar ). In particular, the gamma value is set by the "gamma" keyword (see http://apbs.sourceforge.net/doc/user-guide/index.html#apolar-gamma) . -- Nathan > > Thanks, > will > > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2005. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/_______________________________________________ > 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/ |