Hello Nahsivar--
> 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 ?
>
You can accomplish this task using the XPLOR CONStraints INTEraction
statement. From Python this would be e.g.
xplor.command("constr inte (name N and resid 1) (name HN and resid 1) end")
xplor.command("flags exclude * include BOND end")
bondEnergy = xplor.command("energy end",("ENER",))
(or something like this)
I hope this helps--
Charles
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