Hi James,<div>usually people run a minimization using distance restrain on the two atoms in order to </div><div>make them closer.</div><div>Then the obtained cnfiguration is used to recalculate the topology.</div><div><br>
</div><div>Francesco<br><br><div class="gmail_quote">2012/4/28 James Starlight <span dir="ltr"><<a href="mailto:jmsstarlight@gmail.com" target="_blank">jmsstarlight@gmail.com</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Gromacs Users!<br><br>I have a model of my protein wich has 4 S-S bounds in the loop regions. So I want to define in topology all those four S-S linkage.<br><br>Unfortunatelly one of that S-S have not been recognised by Gromacs ( Also I've tried to check this bond in pymol and found that distance between that two Cys Cys are larger for S-S occurence) due to some inaccyracy of model.<br>
<br>Is there any way to define such missing S-S manually? On the gromacs site I've found possible sollution by means of spechbond.dat editing. I've tried to increase distance between S-S atoms but this have not had desirebly affect.<br>
<br>In the topology.top file I've found that the S-S bonds beetween S atoms are defined in the bond section without any type for such bond type. Also I've found that the same enties are present in the angle and dihedralls sections. Could I define the same contact only in the bond section and further minimise my system to obtain new S-S linckage or should I also define all other enties ( like dihedralls etc) for that bond ?<br>
<br><br>Thanks for help<span class="HOEnZb"><font color="#888888"><br><br><br>James<br>
</font></span><br>--<br>
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