.. and the main question- what should be in mdp file of such restrained minimisation ?<br><br>Today I've done vry properly minimisation of such system in vacuum with the CG minimisator and applied disres ( above example ) with big force constant ( disres options have been defined in the minim.mdp file ). As the result I have not noticed any perturbation in the distance between two S-S atoms the distance between wich I've constrained.<br>
<br><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:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Hi Francesco!<br><br>So I must define in the current topology the disres bettwen two S atoms ( in the below example 1 and 10 ) to apply hormonic restains<br><br><pre>[ distance_restraints ]<br>; ai aj type index type’ low up1 up2 fac<br>
1 10 1 0 1 0.18 0.20 0.22 1.0<br><br>to restrain this atoms within 0.2 nm. Does it correct ? Or should I use some other disres for such task ?<span class="HOEnZb"><font color="#888888"><br><br>James<br></font></span></pre>
<div class="HOEnZb"><div class="h5"><br><br><div class="gmail_quote">2012/4/28 francesco oteri <span dir="ltr"><<a href="mailto:francesco.oteri@gmail.com" target="_blank">francesco.oteri@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">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:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div><div>
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><font color="#888888"><br><br><br>James<br>
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<br clear="all"><div><br></div>-- <br>Cordiali saluti, Dr.Oteri Francesco<br>
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