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On 13/12/2011 11:46, <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a> wrote:
<blockquote
cite="mid:20111213104647.D442425C8A@struktbio205.bmc.uu.se"
type="cite">
<pre wrap="">
Message: 1
Date: Tue, 13 Dec 2011 17:10:01 +1100
From: Mark Abraham <a class="moz-txt-link-rfc2396E" href="mailto:Mark.Abraham@anu.edu.au"><Mark.Abraham@anu.edu.au></a>
Subject: Re: [gmx-users] Force field for polymer molecule - tips
To: Discussion list for GROMACS users <a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a>
Message-ID: <a class="moz-txt-link-rfc2396E" href="mailto:4EE6EC39.2090604@anu.edu.au"><4EE6EC39.2090604@anu.edu.au></a>
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On 13/12/2011 5:06 PM, Jernej Zidar wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi.
I would like to use a CHARMM (CGennFF based) of polymer molecule in
Gromacs. The polymer is composed of three different monomer and two
different terminal residues (one for each of the the two terminals) -
five residues in total.
The CHARMM generalized FF has already been ported to Gromacs so
judging from the documentation
(<a class="moz-txt-link-freetext" 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>)
I should create a monomeres.rtp (arbitrary name?) file containing the
information about the monomeres. Any tips on doing that?
The general workflow will be:
Generate the initial structure of the polymer of a given composition
using Charmm* and save the coordinates as a PDB (plus two other
files). Then supply the generated PDB to pdb2gmx to generate the
initial GRO file.
Second question:
How will pdb2gmx "know" it has to parse the monomeres.rtp file?
</pre>
</blockquote>
<pre wrap="">It can't. You must add to an existing .rtp file.
Mark
</pre>
</blockquote>
I will add that you will also have to add the residue to
aminoacids.dat file, so that the polymer repeat unit is recognized.
for your small polymer molecule you can just generate from the
swissparam website<br>
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