AMBER Archive (2004)

Subject: Re: AMBER: About TI with sander

From: Guanglei Cui (
Date: Mon Jun 28 2004 - 14:46:52 CDT

Hi, Chunhu

1. you need to define dummy atoms for atoms that disappear, for example,
DH (dummy hydrogen)
2. in the tutorial page you referred, the last column is pert.charge,
which is the atomic charge for the perturbed state. in amber8, it's the
delta.charge, which is the difference between lambda=0 and lambda=1, if
I understand it correctly.


Chunhu Tan wrote:

> I am a new comer of AMBER, and I want to calculate free energy change
> with sander TI (AMBER8), but I have some "simple" questions, so, could
> you help me?
> 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 ), followed the steps in this page:
> but when I want to saveamberparmpert, leap told me that could not find
> the perturbed type "DH".
> 2) How to calculate the delta.charge? Also in
> that page, the delta.charge of first CB is set to 0.1050, how to get
> this value?
> Thanks in advance!
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