How to effectively calculate particular (pairwise) energy terms such as VdW,
H-bond & electrostatic energies
for a given model/conformation or even in general a PDB structure (a chain from
a simple PDB file) ?
Using MD programs like Gromacs or CHARMM or AMBER one could do it. But since
X-plor also includes the corresponding FF terms it would be possible to easily
evaluate such pairwise terms with more control (in the scripting)
Simply, for interacting residue/atomic pairs, how to evaluate corresponding
energies (from a given FF) particularly H-Bond energies & VdW (L-J potential
energies). If this is not straightforward, where does one find the appropriate
parameters ?
Thanks in advance.
nahsivar
_______________________________________________
Xplor-nih mailing list
[email protected]
http://cake.cit.nih.gov/mailman/listinfo/xplor-nih
