In most cases (it is form predicted structures) if the bonds is not formes, the S atoms are at the opposite side of the backbone. And I work on peptides, so the length of the structure isn't that big (50 residues max)<br clear="all">
<div><br></div><div>--------------------------</div><br><div>Pierre THEVENET</div><div>Ph.D. Candidate</div><div>INSERM - MTi</div><div>Ecole Doctorale B3MI</div><div>Université Paris Diderot - Paris 7</div><div><br></div>
<br>
<br><br><div class="gmail_quote">2012/4/10 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im"><br>
<br>
Pierre THEVENET wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
How long the MD simulation should be? The problem is that I run multiple simulation (a hundred at a time) and the MD are really time consuming. I should probably can't do it, if the time you propose is too long, I probably forget it.<br>
<br>
</blockquote>
<br></div>
I can't predict how much time it would take. How far apart are the S atoms from one another? If it's just a small distance beyond the normal cutoff, it should be quick, a few hundred ps or less (assuming everything else is otherwise stable). If the distance is very long and would require large structural transitions to accommodate, then you're probably in trouble.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
Thank you<br>
<br>
--------------------------<br>
<br>
Pierre THEVENET<br>
Ph.D. Candidate<br>
INSERM - MTi<br>
Ecole Doctorale B3MI<br>
Université Paris Diderot - Paris 7<br>
<br>
<br>
<br>
<br></div>
2012/4/10 Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>><div class="im"><br>
<br>
<br>
<br>
<a href="mailto:pithevenet@free.fr" target="_blank">pithevenet@free.fr</a> <mailto:<a href="mailto:pithevenet@free.fr" target="_blank">pithevenet@free.fr</a>> wrote:<br>
<br>
<br>
Here is what I have done:<br>
<br>
First, I created the .gro file with the command line:<br>
pdb2gmx -f test.pdb -o test.gro -p test.top -ignh -missing<br>
<br>
<br>
Then, I added at the end of my test.top file the following lines<br>
(I double checked the atom numbers):<br>
<br>
[ distance_restraints ]<br>
; ai aj type index type' low up1 up2 fac<br>
37 140 1 0 1 0.19 0.21 0.22 1<br>
<br>
then, I done:<br>
editconf -f test.gro -o test-box.gro -d 2.0 -c -bt cubic<br>
<br>
grompp -c test-box.gro -p test.top -o test-min.tpr -f test-em.mdp<br>
<br>
mdrun -s test-min.tpr -c test-min.gro -deffnm test-min -v -nice 0<br>
<br>
<br>
and finally get my new pdb file with:<br>
<br>
editconf -f test-min.gro -o test-min.pdb<br>
<br>
But it didn't seemed it had make the two sufur atom closer than<br>
if I didn't add the distance_restrain in the top file.<br>
<br>
Did I do something wrong?<br>
<br>
<br>
Simple energy minimization is unlikely to give rise to the<br>
structural changes you need to bring these atoms close together.<br>
Running a short MD simulation may work, though if the atoms are<br>
very far apart and you force them together quickly, you may have<br>
stability issues.<br>
<br>
<br>
-Justin<br>
<br></div>
-- ==============================<u></u>__==========<div class="im"><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></div>
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</blockquote><div class="HOEnZb"><div class="h5">
<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> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
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