As I understood the APBs plugin which already exist in PyMol is the very efficient device for electrostatic potential calculations.
2 questions have been arisen: 1- How I could change cut-off distances for the electrostatic? E.g I'd like to consider only interactions within 5 A between any charged groups. 2- What advantages has the usage of pdb2pqr plugin? Also in the pdb2pqr tools options I've found some options for force fields. As I know Poisson-Boltzmann equation on which APBS is based doesnt need any force fields (charge calculation from ab initio principles). Why force fields used here ? 3- IS there other plugins for the electrostatic surface calculation with (1) possibility to change cut-offs and (2) charge assignment from the force fields or ab initio calculations ? Thanks for help, James 2013/3/27 Mike Marchywka <[email protected]>: > > > > I have a similar requirement, taking density and potential dstriutbutions from > jdftx which are written as plain binarry doubles. I use a script and > some code to create an xplor file which seems to work but I have > to adjust the position and scale to let it > overlay the ion positions that I read from an xyz file. > > AFAICT xplor is about the only easy format that pymol takes > but I was debating about trying to find others. i think > I dug through my older version of pymol, went to the > effort of changing it all to c++/extern c and then dropped it. > The xplor approch seems to work well enough for now. > > > Is there an easier way? > Thanks. > > > ---------------------------------------- >> Date: Wed, 27 Mar 2013 13:41:24 +0400 >> From: [email protected] >> To: [email protected] >> Subject: [PyMOL] Electrostatic potential surface >> >> Dear PyMol users! >> >> >> I wounder to know about built-in PyMol option for electrostatic >> potential visualisation. >> >> For example I have pdb coordinates of my protein as well as its >> electrostatic potential distribution (calculated by another software). >> Using MolMol with both of that files I can visualize the electrostatic >> potential surface by means of "PaintSurface" option. Can I do the same >> with the PyMOl? >> >> >> >> Thanks for help, >> >> >> James >> >> ------------------------------------------------------------------------------ >> Own the Future-Intel® Level Up Game Demo Contest 2013 >> Rise to greatness in Intel's independent game demo contest. >> Compete for recognition, cash, and the chance to get your game >> on Steam. $5K grand prize plus 10 genre and skill prizes. >> Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d >> _______________________________________________ >> PyMOL-users mailing list ([email protected]) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/[email protected] > ------------------------------------------------------------------------------ Own the Future-Intel® Level Up Game Demo Contest 2013 Rise to greatness in Intel's independent game demo contest. Compete for recognition, cash, and the chance to get your game on Steam. $5K grand prize plus 10 genre and skill prizes. Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d _______________________________________________ PyMOL-users mailing list ([email protected]) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/[email protected]
