AMBER Archive (2008)

Subject: Re: AMBER: MD of protein-ligand comlex

From: Syed Tarique Moin (
Date: Mon Jan 07 2008 - 00:18:20 CST


Yes you have to create frcmod file for the organic
molecule. because this will give the parameter(bond
length, angle, etc) of organic molcules.


--- umbrita itl <> wrote:

> Hello amber users,
> I have few questions. I am trying to get Molecular
> Dynamic receptor-ligand complex. I have never done
> MD on protein-ligand complex before.
> I am studying Streptavidin/Biotin Tutorial and I
> am confused about how to do it.
> Should I create a " frcmod " file for my system?
> I do not understand why biotin file is prepared in
> leap . I thought, for preparation of ligand we need
> use Antechamber.
> Can someone please help?
> Thank you very much for any sugestions.
> Anna
> ---------------------------------
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