I am sorry, but because antechamber will only work with these atoms: C, N, O, S, P, H, F, Cl, Br and I, so acype won't work for Hg.<div><br></div><div>A "hack" would be to replace Hg by another allowed element. But this is only to give you a hint of what topology and parameters might look like. Then you have to work hard in literature to find parameters and likely make use of RED for getting a more quantum mechanics approach for your parameters and charges.</div>
<div><br></div><div>Good luck,</div><div><br></div><div>Alan</div><div><br><div class="gmail_quote">On 23 November 2011 10:35, madhumita das <span dir="ltr"><<a href="mailto:madhumita.bioinfo@gmail.com">madhumita.bioinfo@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Hi GROMACS users,<br><br> I have used acpype.py to convert parameter and topology file from amber to gromacs but some of the parameters (angle and dihedral)regarding a particular residue having mercury in it was not generating,please help. <br>
Thanks in advance.<span class="HOEnZb"><font color="#888888"><br> Madhumita Das<br>
</font></span><br>--<br>
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