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On 30/01/2012 11:30 PM, Zoe Hall wrote:
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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?</p>
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<br>
Probably not, but you would have to consult the AMBER force field
documentation (i.e. published papers) for an initial answer.<br>
<br>
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<p class="MsoNormal"> 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. </p>
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<br>
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.<br>
<br>
Mark<br>
<br>
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<p class="MsoNormal"><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"><a class="moz-txt-link-abbreviated" href="mailto:zoe.hall@chem.ox.ac.uk">zoe.hall@chem.ox.ac.uk</a><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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