[gmx-users] Re: Assigning protonation states using Amber ff

intra\sa175950 stephane.abel at cea.fr
Tue Jan 31 14:10:03 CET 2012


I suggest taking a look in RED.DB web site
(http://q4md-forcefieldtools.org/REDDB/index.php), where some RESP charges
for DNA are stored. 




Message: 1
Date: Tue, 31 Jan 2012 16:11:02 +1100
From: Mark Abraham <Mark.Abraham at anu.edu.au>
Subject: Re: [gmx-users] Assigning protonation states using Amber ff
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4F2777E6.9030903 at anu.edu.au>
Content-Type: text/plain; charset="iso-8859-1"

On 30/01/2012 11:30 PM, Zoe Hall wrote:
> Dear gromacs users,
> I am carrying out solvent-free simulations of a DNA-protein complex 
> using the Amber forcefield. Amber automatically assigns negative 
> charges to the DNA. Is there any way to have neutral DNA?

Probably not, but you would have to consult the AMBER force field 
documentation (i.e. published papers) for an initial answer.

> Similarly, I would like to select which Arg residues are protonated, 
> however the Amber forcefield does not appear to support deprotonated 
> Arg. Is there any way around this? Previously I have been able to 
> assign the protonation state of all basic and acidic residues with the 
> OPLS forcefield (using the interactive commands in pdb2gmx), however 
> with DNA included, I figured I needed to use Amber.

Different force fields are different. If neutral arginine is correct for 
your system, then you will have to parametrize and make a new .rtp entry 


> Any advice on this would be appreciated!
> Thanks in advance,
> Zoe Hall
> Zoe Hall
> Department of Chemistry
> Oxford University
> _zoe.hall at chem.ox.ac.uk_

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