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On 12/02/2012 4:16 PM, Yao Yao wrote:
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<div>I am simulating a protein in glycerol solution in amber03
ff and followed
<a class="moz-txt-link-rfc2396E" href="http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents">"http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents"</a>.</div>
<div>Since glycerol is not available in amber03.ff by default, I
built it in the ffbonded.itp</div>
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<br>
You should not need to touch this file to model glycerol. There are
no atom or interaction types that are materially different from
those on peptide side chains.<br>
<br>
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<div> and aminoacids.rtp.</div>
<div>For test purpose, I then made a itp for it and solvate it
as a protein and changed .top file accordingly, everything
seems fine when I grompp,</div>
<div>but when I insert it as a co-solvent, it shows like that I
never did claim any bond angles, dihedrals, .... even when I
#include its .itp and change #mols in my new topology.<br>
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<br>
You need to work out what is different in the two cases. The diff
tool can be useful here. There is no fundamental difference in the
.top construction for the two cases you are considering - only in
construction of the initial coordinates.<br>
<br>
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<div><br>
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<div>I guess the problem is if I do not claim the co-solvent as
a protein, ff will not go to ffbonded.itp to recognize the new
interactions.</div>
<div>Is there any other file for co-solvent interactions I need
to change?</div>
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<br>
The ffbonded.itp file is #included regardless of what you name your
moleculetypes. You may not be #including the correct one - but then
again I think you should only have the standard one in the first
place.<br>
<br>
Mark<br>
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