AMBER Archive (2003)

Subject: Re: AMBER: a simple question about HBond energy...

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Fri Dec 12 2003 - 16:16:42 CST

> None of the current Amber force fields have a special H-bond term. As you
> noticed, they treat this as electrostatic and van der Waals. Aside from
> writing new code, there is nothing that you can switch on.

You could develop a new ff using explicit hbonding terms, or as Dave
suggests (I believe) add code to collect the electrostatic and van
der Waals for designated interactions and report this separately.
The latter can also be done using ANAL, creating a group for donors
and a group for acceptors.

Generally what people want to know about hbonding is to what extent
a given hbond exists, which carnal and probably ptraj can determine
from the mdcrd output.

Bill Ross

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