Thread: [Apbs-users] Two separate proteins in one system
Biomolecular electrostatics software
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From: Mazen A. <m....@bi...> - 2007-07-13 13:40:50
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Hello all, I am going to calculate solvation energy for a system of Two separate proteins. I am not sure if APBS will recognize my system as two separate proteins, or It will deal with my system as one protein with dielectric constant for the space between the two proteins as inside a protein ?. Thanks in advances Mazen |
From: Nathan B. <sob...@gm...> - 2007-07-14 00:13:02
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Hello -- If you put both proteins in the same PQR file, then APBS will treat them as a complex. In order to have APBS treat them separately, you'll need to run calculations on PQR files of the separated molecules. Thanks, Nathan On Jul 13, 2007, at 5:50 AM, Mazen Ahmad wrote: > Hello all, > I am going to calculate solvation energy for a system of Two separate > proteins. > > I am not sure if APBS will recognize my system as two separate > proteins, or It will deal with my system as one protein with > dielectric constant for the space between the two proteins as inside a > protein ?. > > Thanks in advances > > Mazen > > > ---------------------------------------------------------------------- > --- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > 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: Karim E. <kar...@ya...> - 2007-07-17 10:08:18
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I'm trying to calculate the solvation free energy for a massive system, I'm using the async option in APBS. Therefore I ran a separate job for each processor. I'm wondering whether the solvation energy is just a simple summation of the output ' Global net energy' or not. if so , how to account for the processor overlap factor 0.1 in this summation ? I tried summing up the resulting ' Global net energy' of each processor , the solvation energy is unusually high (e.g -157859 kj/mol). [ idential grid setup is used for solvent and vaccum calculation with grid spacing of 0.5] your help is very much appreciated. Karim ____________________________________________________________________________________ Yahoo! oneSearch: Finally, mobile search that gives answers, not web links. http://mobile.yahoo.com/mobileweb/onesearch?refer=1ONXIC |
From: Nathan B. <ba...@bi...> - 2007-07-17 17:14:15
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Hello -- The ansynchronous mode of APBS calculations eliminates overlap between processors (since all processor partition/domain information is calculated for all processors at the start of the run). It sounds like the very large energy that you're observing is most likely due to an insufficiently small grid spacing or other problems with location of the protein on the mesh in the reference and solvated PB calculations. I would recommend starting with a simpler system (e.g., a binding energy such as the actin-dimer example) that can be easily tested for convergence with respect to grid spacing. Thanks, Nathan On Jul 17, 2007, at 5:08 AM, Karim Elsawy wrote: > I'm trying to calculate the solvation free energy for > a massive system, I'm using the async option in APBS. > Therefore I ran a separate job for each processor. > I'm wondering whether the solvation energy is just a > simple summation of the output ' Global net energy' > or not. if so , how to account for the processor > overlap factor 0.1 in this summation ? > I tried summing up the resulting ' Global net > energy' of each processor , the solvation energy is > unusually high (e.g -157859 kj/mol). [ idential grid > setup is used for solvent and vaccum calculation with > grid spacing of 0.5] > your help is very much appreciated. > Karim > > > > > > > ______________________________________________________________________ > ______________ > Yahoo! oneSearch: Finally, mobile search > that gives answers, not web links. > http://mobile.yahoo.com/mobileweb/onesearch?refer=1ONXIC -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ |