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On 13/02/2011 11:49 AM, TJ Mustard wrote:
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<p style="margin: 0px;">Hi all,</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">I have been testing the ability of taking
a sphere of a protein around a ligand, and positionally restrain
the specified alpha carbons. I was hoping to keep non connected
protein chains from drifting apart. I have been able to run
these md/fep jobs, but I get huge interaction energies for the
ligand, which has no positional restraints on it. I also don't
restrain any atoms within the rvdw, rcoulomb and rlist radii. Am
I thinking this is a possibility when it is physically
impossible to simulate?</p>
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<br>
I doubt it.<br>
<br>
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cite="mid:2023151886.17848.1297558145062.JavaMail.open-xchange@oxusgw01.lxa.perfora.net"
type="cite">
<p style="margin: 0px;">Currently I am selecting all residues
around the ligand that have an atom within 20 Angstroms. I then
save this as a pdb file and then run it through pdb2gmx,
manually create a posres.itp file for each "chain" with their
first and last residue's alpha carbon. Once I turn off these
positional restraints the FEP energies drop down to "normal"
levels.</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">Does anyone have an idea what is
happening?</p>
<br>
And if you do, can you please give a recommendation?<br>
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<br>
I'd guess you're not restraining how you think you are :-) Bear in
mind that position restraints are indexed relative to a
[moleculetype] (and must be #included there), and not the whole
system.<br>
<br>
The combination of g_select and genrestr is probably a more reliable
and documentable way to generate your position restraints.<br>
<br>
Mark<br>
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