VMD-L Mailing List

From: Himanshu Khandelia (hkhandel_at_memphys.sdu.dk)
Date: Fri Jan 19 2007 - 07:41:54 CST

In addition, you can take your dcds to charmm, which has an explicit
function to calculate h-bonding energy. You will need the par_hbond.inp
file. Check the charmm documentation hbonds.inp. But it might be easier to
do what Peter suggests if you are not familiar with charmm

> Hi Amit,
> this depends on what you mean by hbond energy. If you're using a modern
> CHARMM forcefield, there *is* no hbond energy -- they're implicit in the
> electrostatic and VDW interactions. You can use namdenergy to get the
> nonbond interactions between these residues, or write your own script to
> take the coordinates in vmd and run them through an arbitrary energy
> function over the trajectory.
>
> Peter
>
> amit dong wrote:
> >
> > Hi,
> > I need to calculate H-bond energy between a pair of residues for the
> > whole trajectory. I was wondering if there is any quick way of doing it.
> > Thanks
> > Amit
>