AMBER Archive (2004)

Subject: Re: AMBER: About TI with sander

From: David A. Case (
Date: Tue Jun 29 2004 - 11:45:52 CDT

On Mon, Jun 28, 2004, Chunhu Tan wrote:

> 1) How to tell leap that certain atoms disappeared? For
> example, when val changes to ala, I change the methyls (CT,HC,HC,HC) to
> hydrogens (HC, DH,DH,DH ),
> but when I want to saveamberparmpert, leap told me that could not find
> the perturbed type "DH".

You need to create a "frcmod" file that give the properties of the DH atom
(e.g. zero vdw parameters, bond and angle parameters that correspond to the
a "real" H atom...)

> 2) How to calculate the delta.charge?

You have, from the Amber library, the charges for alanine and for valine.
The delta.charge is just the difference between these.

...good luck....dac

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