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Hi James,<br>
usually I insert by hand a bond in the topology file between the two
atoms and then I minimize.<br>
This bond doesn't cause the generataion of angles and dihedrals,
butit is enough to make the atom closer.<br>
<br>
Francesco<br>
Il 28/04/2012 16:08, James Starlight ha scritto:
<blockquote
cite="mid:CAALQopwbST9KupOOHRGPVXMJT3jzEfKSCQb4fjqNUMFf167cSA@mail.gmail.com"
type="cite">.. 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 moz-do-not-send="true"
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 ]
; ai aj type index type’ low up1 up2 fac
1 10 1 0 1 0.18 0.20 0.22 1.0
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">
James
</font></span></pre>
<div class="HOEnZb">
<div class="h5"><br>
<br>
<div class="gmail_quote">2012/4/28 francesco oteri <span
dir="ltr"><<a moz-do-not-send="true"
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 moz-do-not-send="true"
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>
</font></span><br>
</div>
</div>
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<span><font color="#888888"><br>
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-- <br>
Cordiali saluti, Dr.Oteri Francesco<br>
</font></span></div>
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