VMD-L Mailing List

From: Sanjeev B.S. (sanjeev_at_mbu.iisc.ernet.in)
Date: Sat Oct 02 2004 - 00:20:11 CDT

> I ONLY want to follow from a trajectory file the HBonds/Dynamics Bonds
> between protein and water (colored in say red) and protein and ions
> (colored say blue) but not the HBonds/DynamicBonds within the
> protein or between water molecules.

I faced a similar problem as VMD does not distinguish between donor and
acceptor. So first I made a list of all hydrogen bonds found, then picked
the atom and residue pairs, and made a H-bond between the two. Tiresome,
but then I had lot of scripts to select the few particular h-bonds I was
interested in, so it was not a big problem. But this is a cumbersome
solution, and should be avoided whenever possible.

But if you wish to do the same using amber tools, I can send you some
tips.