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 [email protected]
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