Thread: [Apbs-users] PDB2PQR generated input on vmd
Biomolecular electrostatics software
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From: Cesar M. <pac...@gm...> - 2007-05-19 01:47:52
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Hi everyone, I would like to do a few apbs calculations using VMD. I would like to make you a few questions: + Is it possible to use pdb2pqr.py generated inputs to run apbs under VMD? I was looking a pdb2pqr.py generated input and the values for cglen and fglen were distinct from those on the apbs plugin. + Do you think that is possible to use apbs plugin to do the analysis of a few structures iterative? or is it better to do the analysis outside of VMD and after load the potentials maps on VMD? Thank you for any help. --=20 ########### "There is no form of prose more difficult to understand and more tedious to= read than the average scientific paper." -- Francis Crick, "The Astonishing Hypothesis" ########### C=E9sar Mill=E1n Pacheco Facultad de Ciencias Universidad Autonoma del Estado de Morelos Tel: 777 3297020 Fax: 777 3207040 email: cm...@se... pac...@gm... |
From: Nathan B. <ba...@cc...> - 2007-05-22 18:33:31
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Hi Cesar -- > + Is it possible to use pdb2pqr.py generated inputs to run apbs under > VMD? I was looking a pdb2pqr.py generated input and the values for > cglen and fglen were distinct from those on the apbs plugin. Not that I'm aware of; however, I think that's a great suggestion and =20= will definitely pass it along. > + Do you think that is possible to use apbs plugin to do the analysis > of a few structures iterative? or is it better to do the analysis > outside of VMD and after load the potentials maps on VMD? I know that VMD has a rich scripting environment which might make =20 something like this feasible. However, I'm not an expert and would =20 suggest you inquire about this on the VMD mailing list. It is =20 certainly possible to do the analyses outside of VMD and load the =20 resulting potentials into VMD. Thanks, Nathan > Thank you for any help. > > --=20 > ########### > "There is no form of prose more difficult to understand and more =20 > tedious to read > than the average scientific paper." > -- Francis Crick, "The Astonishing =20 > Hypothesis" > > ########### > > C=E9sar Mill=E1n Pacheco > Facultad de Ciencias > Universidad Autonoma del Estado de Morelos > Tel: 777 3297020 > Fax: 777 3207040 > email: cm...@se... > pac...@gm... > > ----------------------------------------------------------------------=20= > --- > 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/ |