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Yuhua Song wrote:<br>
<blockquote type="cite" cite="mid00fd01c3dfa5$1afd1f60$313efc80@mojave">
<pre wrap="">Could I get some hints for manually getting the all atom topology based on
united atom topology? or I could not try to get all atom topology based on
united atom topology? or I can borror some parameter from the existing
force field?
Thanks,
Yuhua
----- Original Message -----
From: "David" <a class="moz-txt-link-rfc2396E" href="mailto:spoel@xray.bmc.uu.se"><spoel@xray.bmc.uu.se></a>
To: <a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a>
Sent: Tuesday, January 20, 2004 3:20 PM
Subject: Re: [gmx-users] How to get the all atom topology file for
smallmolecule?
</pre>
<blockquote type="cite">
<pre wrap="">On Tue, 2004-01-20 at 22:59, Yuhua Song wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi, everyone:
I had got the united atom topology file for the small molecule using
</pre>
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</blockquote>
<pre wrap=""><!---->PRODRG.
</pre>
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<blockquote type="cite">
<pre wrap="">Because of the project request, I need to get the all-atom topology of
</pre>
</blockquote>
</blockquote>
<pre wrap=""><!---->the
</pre>
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<blockquote type="cite">
<pre wrap="">small molecule used for the analysis. Could someone give me some
</pre>
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</blockquote>
<pre wrap=""><!---->suggestions
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">about how could I get the all atom topology of small molecule based on
</pre>
</blockquote>
</blockquote>
<pre wrap=""><!---->the
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">united atom topology? or there are some other ways for me to get the all
atom topology file of small molecule?
</pre>
</blockquote>
<pre wrap="">Not with a gromacs tool. Manually...
</pre>
<blockquote type="cite">
<pre wrap="">Thank you very much,
Yuhua
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</pre>
</blockquote>
<pre wrap="">--
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
<a class="moz-txt-link-abbreviated" href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a class="moz-txt-link-abbreviated" href="mailto:spoel@gromacs.org">spoel@gromacs.org</a> <a class="moz-txt-link-freetext" href="http://xray.bmc.uu.se/~spoel">http://xray.bmc.uu.se/~spoel</a>
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<pre wrap=""><!---->
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</blockquote>
Hi Yuhua<br>
<br>
I need to build a topology manualy and it was a hard work, but after
you do the first one you will see that the work is not so hard.<br>
You can look at file ffoplsaa.atp and find the atom types that are
better for your molecule. After this, you can add a new fragment in
ffoplsaa.rpt with this atom types you choose. Now you can use a pdb
file of your molecule with pdb2gmx and get your topology.<br>
<br>
[]'s<br>
<pre cols="72" class="moz-signature">--
Alexandre Suman de Araujo
<a class="moz-txt-link-abbreviated" href="mailto:asaraujo@if.sc.usp.br">asaraujo@if.sc.usp.br</a>
UIN: 6194055
IFSC - USP - São Carlos - Brasil</pre>
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