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Can you cut your molecule into smaller pieces and then join them?<br>
As you only have ten residues more than permitted, another option is to
use for example H instead acetate, etc... After creating the topology
just change this.<br>
Hope this help,<br>
Cheers,<br>
Ruben<br>
<br>
Osmany Guirola Cruz wrote:<br>
<blockquote type="cite"
cite="midE78E51BB7B45C749B11C8B5BA64107E10849C7B8@mercurio.cigb.edu.cu">
<pre wrap="">I have a "drug" greater than 300 atoms what should I do to get the
topology
I don know if exist another program or server that do something similar
My drug have 310 atoms
Help please :-(
-----Original Message-----
From: Daan van Aalten [<a class="moz-txt-link-freetext" href="mailto:vdava@davapc1.bioch.dundee.ac.uk">mailto:vdava@davapc1.bioch.dundee.ac.uk</a>]
Sent: Wednesday, May 19, 2004 9:58 AM
To: Peter Zoon
Cc: Discussion list for GROMACS users
Subject: Re: [gmx-users] PRODRG
Peter
You are confusing topology with conformation. For each bond between a
pair of atoms there is a choice of several hundreds of bond types, which
are associated with a) specific force constants and b) specific
equilibrium values (i.e. bond lengths). Same for bond angles. You can
minimize coordinates, but the topology stays the same.
Writing out a G96 FF topology is probably only a day's work if I can
have a full day's use of a G96 FF guru for advice and testing - and of
course everyone is busy!
cheers
Daan
On Wed, 19 May 2004, Peter Zoon wrote:
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">The atom types aren't the problem but the manual conversion of
bonds/angles/dihedrals to G96 types. IMHO this may be intricate in
some cases. I guess it would be very nice to have a G96 topology
automatically generated by PRODRG, the GMX force field seems to be
considered rather outdated even by the Gromacs crew themselves.
</pre>
</blockquote>
<pre wrap="">That doesn't matter right?
If you do a minimization (after you changed to the right atom-types),
the system will just equilibrate and you will reach the right topology
</pre>
</blockquote>
<pre wrap=""><!---->
</pre>
<blockquote type="cite">
<pre wrap="">automatically.
Or am I making a reasoning error here?
Peter
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<pre wrap=""><!---->
########################################################################
######
Dr. Daan van Aalten Wellcome Trust RCD Fellow /
Reader
Wellcome Trust Biocentre, Dow Street TEL: ++ 44 1382 344979
Div. of Biol.Chem. & Mol.Microbiology FAX: ++ 44 1382 345764
School of Life Sciences E-mail: see WWW page
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<pre class="moz-signature" cols="72">--
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Ruben Martínez-Buey. PhD student.
Protein Function and Structure
Centro de Investigaciones Biológicas
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