Try "genbox -cp *.gro -ci dmso.gro -p *.top -o *.gro"<br>Gro file for dmso comes built-in with gromacs 3.3. As Justin has directed, forcefields do matter.<br>
<br>
<br><div><span class="gmail_quote">On 19/08/2008, <b class="gmail_sendername">Justin A. Lemkul</b> <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<span class="q"><br>
<br>
prasun kumar wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
dear users<br>
I am trying to run the simulation fo a protein/DMSO system,Its working
well till genbox but while running GROMPP I am gettin a fatal
error,which is<br>
atom type 'SD' not found.<br>
SD is given in the gro & itp file of DMSO.<br>
what should I do to overcome this problem........<br>
I have tried by replacing SD by S,but its of no use<br>
I should generate a separate top file for DMSO and then include it in the topology file generated for protein<br>
I tried to do this also using PDB2GMX command but again I am gettin error related to 'SD'<br>
</blockquote>
<br></span>
Which force field are you using? If you look at the .rtp entry
(if present), it will tell you the correct atomic nomenclature.
Otherwise, you have an inconsistency in the atomtypes definition
in your topology.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><span class="q">
please help me..........<br>
regards &thanx in advance<br>
<br>
-- <br>
PRASUN (ASHOKA)<br>
<br>
<br></span>
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-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">vt.edu</a> | (540) 231-9080<br>
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