Hi Yegor,<br>
<br>
Are you sure that the negative charges on the *-S-(C=O)-* are the cause
of the trouble? The S and O should be interacting through bonded terms,
notably the angle, and not be influenced by the charges. 1-3
interactions (nonbonded) are by default excluded. Was your starting
structure reasonable and did you perform energy minimization?Did grompp give any warnings? <br><br>
Cheers,<br>
<br>
Tsjerk<br>
<br><div><span class="gmail_quote">On 2/8/06, <b class="gmail_sendername">Yegor Isakov</b> <<a href="mailto:yegoris@yahoo.com">yegoris@yahoo.com</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;">
<br><br>--- Yegor Isakov <<a href="mailto:yegoris@yahoo.com">yegoris@yahoo.com</a>> wrote:<br><br>> I appresiate help from anybody.<br>> I have designed myself topology for a molecule where<br>> cysteine is connected to another chain through
<br>> carbonyl group<br>> (oneChain-S-CO-anotherChain). Negative electrostatic<br>> charges on S and O atoms blow out my molecule within<br>> several cycles. grompp.mdp file contains more or<br>> less<br>> general parameters I used in previous simulation of
<br>> proteins.<br>> Thanks in advance.<br>> Yegor<br>><br>> __________________________________________________<br>> Do You Yahoo!?<br>> Tired of spam? Yahoo! Mail has the best spam<br>> protection around
<br>> <a href="http://mail.yahoo.com">http://mail.yahoo.com</a><br>><br><br><br>__________________________________________________<br>Do You Yahoo!?<br>Tired of spam? Yahoo! Mail has the best spam protection around
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Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<br>Dept. of Biophysical Chemistry<br>University of Groningen<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336<br>