Dear Faez,
I suggest working through the tutorials on
http://ambermd.org/tutorials/
this will give you an understanding of how AMBER works and should give you
the grounding you need to start running MD simulations of proteins.
All the best
Ross
From: Faez Iqbal khan <khanfaeziqbal.gmail.com>
Date: Sunday, November 11, 2012 11:22 PM
To: Ross Walker <ross.rosswalker.co.uk>
Subject: Re: Urgent
Thank you Sir,
I want to Simulate a Protein generated computationally.
Can you help me please. :)
On Mon, Nov 12, 2012 at 9:17 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Dear Faez,
>
> Antechamber is NOT designed to be used for an entire protein. It is designed
> to be used for individual ligands and / or cofactors. What is your reasoning
> behind wanting to use it on an entire protein rather than using one of the
> amino acid force fields such as ff99sb?
>
> Have you looked at the following tutorial?
>
> http://ambermd.org/tutorials/basic/tutorial4b/
>
> All the best
> Ross
>
>
> From: Faez Iqbal khan <khanfaeziqbal.gmail.com>
> Date: Sunday, November 11, 2012 11:14 PM
> To: <amber.ambermd.org>, <amber-admin.biomaps.rutgers.edu>,
> <amber-owner.ambermd.org>
> Subject: Urgent
>
> How Sir,
> I am running Antechamber for a protein (mol2 file as well as PDB file).
>
> Error: Info: the atom number exceeds the MAXATOM, reallocate memory
> automatically.
>
> Please Help Me.
>
>
> Faez Iqbal Khan
> PhD
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Received on Sun Nov 11 2012 - 23:30:02 PST
