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On 16/06/2012 5:31 PM, delara aghaie wrote:
<blockquote
cite="mid:1339831887.34607.YahooMailNeo@web28702.mail.ir2.yahoo.com"
type="cite">
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<div><span>Dear Gromacs Users</span></div>
<div><span><br>
</span></div>
<div><span>Running pdb2gmx on a pdb file containing a dimer
protein, I used option (( chainsep id_or_ter)))</span></div>
<div><span>This resulted in separated topologies for each chain
and separated posre files. Also in the .gro file, the
aminoacides of the second chain started from number 1.
(Without this option the second chain aminoacides will
receive numbers in continuation of numbers of first
chain))....</span></div>
<div><br>
<span></span></div>
<div><span>Now:</span></div>
<div><span>Can I use these files to continue the simulations or
again it is necessary to follow the procedure explained in
multiple chains gromacs???</span></div>
<br>
</div>
</blockquote>
<br>
By definition of pdb2gmx function, you now have a topology and a
coordinate file that matches. That is the minimum requirement for
grompp to succeed later. grompp doesn't care about some aspects of
atom numbering - including your observation above.<br>
<br>
Mark<br>
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