AMBER Archive (2008)

Subject: Re: AMBER: solvent interaction in active site

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Sep 01 2008 - 08:49:20 CDT

I think you need to be much more specific about what you want.
have you done any of the tutorials? they might help. you might also
want to read the ptraj manual carefully, it has lots of analysis
information. it's hard for others to tell you what you should look for
in your system. you might try checking hydrogen bonds between active
site residues and water, or looking at a trajectory showing only water
close to active site residues, or looking at water densities in the
active site. all of these and more are possible in ptraj, so I
encourage you to read the manual and then ask us specific questions
about using those commands if the manual is not clear.

On Wed, Aug 27, 2008 at 10:41 PM, Hakkim Boy <vhakkim_at_yahoo.co.in> wrote:
> dear amber users,
>
> I have run the MD of metalloprotein, now I want to know
> how the solvent molecule interact with active site residues but i dont know
> how to give input command in anber 9.0 can any one help me. Thank you.
>
> with regards
>
> V. Hakkim
> Junior Research Fellow
> Chemical laboratory
> Central leather research institute
> Adyar
> Chennai-20
> Mobile No:9791041235
> ________________________________
> Unlimited freedom, unlimited storage. Get it now
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