[gmx-users] Assigning protonation states using Amber ff

Zoe Hall zoe.hall at chem.ox.ac.uk
Mon Jan 30 13:30:59 CET 2012

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? 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.

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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