Hi Aneesh,
Thanks for the useful link.
I was mainly concerned about positioning of acetic acid
molecules around the DAcPC and force field. Anyhow I accomplished them using
Sybyl for positioning the acetic acid and antechamber (using GAFF) for creating
input files. I was able to
run MD successfully.
thanks,
Senthil
________________________________
From: aneesh cna <aneeshcna.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Fri, June 3, 2011 12:56:56 AM
Subject: Re: [AMBER] simulation of small molecule with organic solvent and water
Hi Senthil,
You can use Packmol (
http://www.ime.unicamp.br/~martinez/packmol/) for
setting up system for MD simulations.
All the best
Aneesh
On Thu, Jun 2, 2011 at 11:03 AM, Senthil Natesan <sen.natesan.yahoo.com>wrote:
> Hello Amber Users/Developers,
>
> Greetings. I want to run MD simulation of diacetyl phosphocholine along
> with 4
> acetic acid molecules in explicit water.
> I did run MD simulation without acetic acid successfully. Can anyone
> point me
> to any older posts ( I am not able to find any relevant posts).
> or tutorials (or papers) to accomplish the above task?
>
> thanks in advance,
>
> Senthil Natesan
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Jun 03 2011 - 07:30:02 PDT
