[gmx-users] Assigning protonation states using Amber ff

[Mark Abraham]

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 
accordingly.

Mark

> 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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