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On 7/05/2011 7:16 PM, Mr Bernard Ramos wrote:
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<div>Thanks for the response. I will be doing a simple MD
without the positional restraints. How do I go about
reviewing the code for posres? What I did was to add new
ff parameters for a new residue I introduced. May I
please know what file in the program determines the
posres so that I can revew them. Thanks.</div>
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<br>
Please give full descriptions the first time. I posted a noob
question on the AMBER mailing list a few months back, and would
never have gotten the problem solved except that I included some
details that I thought were irrelevant, and someone spotted my
problem. We've all got better things to do than play
question-and-answer. You might have invented some atom names that
pdb2gmx doesn't know how to cope with - but you haven't said whether
your apparently erronously generated position restraints are
specific to your new residue or not. Unfortunately you haven't
shared your atom names after I suggested the atom names were
probably the problem, and I'm not going to make guesses. There's
various databases in $GMXLIB/share/top for various force fields, but
I don't know your GROMACS version either...<br>
<br>
I don't think looking at the code will lead to a solution.<br>
<br>
Mark<br>
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<div>--- On <b>Sat, 5/7/11, Mark Abraham <i><a class="moz-txt-link-rfc2396E" href="mailto:Mark.Abraham@anu.edu.au"><Mark.Abraham@anu.edu.au></a></i></b>
wrote:<br>
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From: Mark Abraham <a class="moz-txt-link-rfc2396E" href="mailto:Mark.Abraham@anu.edu.au"><Mark.Abraham@anu.edu.au></a><br>
Subject: Re: [gmx-users] On posre.itp<br>
To: "Discussion list for GROMACS users"
<a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a><br>
Date: Saturday, May 7, 2011, 5:10 PM<br>
<br>
<div id="yiv1037510764">On 7/05/2011 7:01 PM, Mr Bernard
Ramos wrote:
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<div>Hi everyone!</div>
<div> </div>
<div>I was able to generate a pdb file in
which the hydrogens for the molecule are
already included (that way I avoided using
the hdb file for the pdb2gmx). However,
when I checked the posre.itp, the some of
the restraints were applied to the
hydrogens. Is this correct because I am
not sure since I what I know is that the
restraints should be applied to heavy
atoms.</div>
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<br>
Maybe your atom names are confusing pdb2gmx. Maybe
you're comparing apples and oranges with the indices
in the coordinate file and the indices in the
posres.itp (which are relative to the [atoms], IIRC).<br>
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<div>Are the positional restraints needed
only for the equalibration step but not
for the production runs in normal MD
simulations. Thanks. </div>
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<br>
Up to you. Do you want to sample under unphysical
restraints or not?<br>
<br>
Mark<br>
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