Francesco,<br><br>Thanks, I find your aproach very handfull :)<br><br>Justin,<br><br>in that example I've defined in minim.mdp<br><br><b>disre = simple<br><br></b><b><a name="nmr"><b>disre_f = 5000<br><br>in the topology.top I've included<br>
<br></b></a></b> [ 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>where 1 and 10 the numbers of the S atoms of both Cys residues. and 0.2 is the disered distance between wich I want to obtain after such minimisation.<br><b><b><br><br>
<br>As the consequence no changes have been detected after such CG minimisation :( What I've forgotten ?<br><br>James<br><br><br></b></b><div class="gmail_quote">2012/4/28 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</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 class="im"><br>
<br>
On 4/28/12 10:08 AM, James Starlight wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
.. and the main question- what should be in mdp file of such restrained<br>
minimisation ?<br>
<br>
Today I've done vry properly minimisation of such system in vacuum with the CG<br>
minimisator and applied disres ( above example ) with big force constant (<br>
disres options have been defined in the minim.mdp file ). As the result I have<br>
not noticed any perturbation in the distance between two S-S atoms the distance<br>
between wich I've constrained.<br>
<br>
</blockquote>
<br></div>
You need to add the applicable distance restraint settings for them to be utilized.<br>
<br>
<a href="http://manual.gromacs.org/online/mdp_opt.html#nmr" target="_blank">http://manual.gromacs.org/<u></u>online/mdp_opt.html#nmr</a><br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<br>
<br>
2012/4/28 James Starlight <<a href="mailto:jmsstarlight@gmail.com" target="_blank">jmsstarlight@gmail.com</a> <mailto:<a href="mailto:jmsstarlight@gmail.com" target="_blank">jmsstarlight@gmail.com</a><u></u>>><div class="im">
<br>
<br>
Hi Francesco!<br>
<br>
So I must define in the current topology the disres bettwen two S atoms ( in<br>
the below example 1 and 10 ) to apply hormonic restains<br>
<br>
[ distance_restraints ]<br>
; ai aj type index type’ low up1 up2 fac<br>
<br>
<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 ?<br>
<br>
James<br>
<br>
<br>
<br>
2012/4/28 francesco oteri <<a href="mailto:francesco.oteri@gmail.com" target="_blank">francesco.oteri@gmail.com</a><br></div>
<mailto:<a href="mailto:francesco.oteri@gmail.com" target="_blank">francesco.oteri@gmail.<u></u>com</a>>><div class="im"><br>
<br>
Hi James,<br>
usually people run a minimization using distance restrain on the two<br>
atoms in order to<br>
make them closer.<br>
Then the obtained cnfiguration is used to recalculate the topology.<br>
<br>
Francesco<br>
<br>
2012/4/28 James Starlight <<a href="mailto:jmsstarlight@gmail.com" target="_blank">jmsstarlight@gmail.com</a><br></div>
<mailto:<a href="mailto:jmsstarlight@gmail.com" target="_blank">jmsstarlight@gmail.com</a><u></u>>><div class="im"><br>
<br>
Dear Gromacs Users!<br>
<br>
I have a model of my protein wich has 4 S-S bounds in the loop<br>
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 (<br>
Also I've tried to check this bond in pymol and found that distance<br>
between that two Cys Cys are larger for S-S occurence) due to some<br>
inaccyracy of model.<br>
<br>
Is there any way to define such missing S-S manually? On the gromacs<br>
site I've found possible sollution by means of spechbond.dat<br>
editing. I've tried to increase distance between S-S atoms but this<br>
have not had desirebly affect.<br>
<br>
In the topology.top file I've found that the S-S bonds beetween S<br>
atoms are defined in the bond section without any type for such bond<br>
type. Also I've found that the same enties are present in the angle<br>
and dihedralls sections. Could I define the same contact only in<br>
the bond section and further minimise my system to obtain new S-S<br>
linckage or should I also define all other enties ( like dihedralls<br>
etc) for that bond ?<br>
<br>
<br>
Thanks for help<br>
<br>
<br>
James<br>
<br>
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</div></blockquote>
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
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==============================<u></u>==========<div class="HOEnZb"><div class="h5"><br>
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