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On 8/03/2012 12:19 AM, Kavosh Zandsalimi wrote:
<blockquote cite="mid:WC20120307131901.430059@ibb.ut.ac.ir"
type="cite">
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<div class="MsoNormal" style="color: rgb(0, 0, 0); font:
normal normal normal 10pt/normal Arial; text-align:
justify; ">Dear GMX users;</div>
<div class="MsoNormal" style="color: rgb(0, 0, 0); font:
normal normal normal 10pt/normal Arial; text-align:
justify; "> </div>
<div class="MsoNormal" style="color: rgb(0, 0, 0); font:
normal normal normal 10pt/normal Arial; text-align:
justify; ">I hope you are well.</div>
<div class="MsoNormal" style="color: rgb(0, 0, 0); font:
normal normal normal 10pt/normal Arial; text-align:
justify; ">I want to simulate the interactions between DNA
and Ag clusters. The problem is that Amber99 ff does not
know silver atoms and residues.</div>
<div class="MsoNormal" style="color: rgb(0, 0, 0); font:
normal normal normal 10pt/normal Arial; text-align:
justify; ">I have defined Ag and Au in atomtypes.atp and
assigned Ag LJ parameters in ffnonbonded.itp. But I cannot
find out how to define new residues.</div>
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<br>
<a
href="http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field">http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field</a><br>
<br>
Mark<br>
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