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<p class=MsoNormal>Dear gromacs users, <o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>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. <o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Any advice on this would be appreciated!<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Thanks in advance, <o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Zoe Hall<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Zoe Hall <o:p></o:p></p>
<p class=MsoNormal>Department of Chemistry<o:p></o:p></p>
<p class=MsoNormal>Oxford University<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><u><span style='color:#4D54DB'>zoe.hall@chem.ox.ac.uk<o:p></o:p></span></u></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
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