?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 -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://cake.cit.nih.gov/pipermail/xplor-nih/attachments/20140414/b54fcbaa/attachment.html>
