Thank you for the template script to calculate vdW energies of interacting pairs of atoms from a given PDB file. I'll try to extend it to calculate other energies such as hydrogen bond energy etc., Are there ways to use different forcefields for the same calculations ?
On Thursday, April 17, 2014 3:18 PM, Charles Schwieters <charles at schwieters.org> wrote: Hello Nahsivar-- > Thank you, Dr. Scwhieters. I'm yet to get this working though.? If > you would be kind enough to show it from the loading of a PDB file > to calculating most pairwise interaction energies (intra-chain ) > primarily HBond, VdW & may be electrostatics, it would be great.? As > am new to applying Xplor for such purposes, this will be a good > start.? Moreover, as I found out there are not great many tools that > does this simple energy evaluation that is so regularly done and > hence this example could serve a general purpose as well. Please see the small attached script. It prints out all pairs of atoms with vdw energies greater than a tolerance. It isn't so fast, but will hopefully get you started. Charles -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://cake.cit.nih.gov/pipermail/xplor-nih/attachments/20140422/aa173563/attachment.html>
