<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Hello Gaurav,<br>Thanks for your reply,<br>I did position restrained enegry minimisation, and used following .mdp file for the same<br><br>title = protein<br>cpp = /usr/bin/cpp ; the c pre-processor<br>define = -DPOSRE<br>constraints = none<br>integrator = steep<br>dt = 0.002 ; ps !<br>nsteps = 1000<br>nstlist =
10<br>ns_type = grid<br>rlist = 0.9<br>coulombtype = PME<br>rcoulomb = 0.9<br>rvdw = 0.9<br>fourierspacing = 0.12<br>fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>pme_order = 4<br>ewald_rtol = 1e-5<br>optimize_fft = yes<br>;<br>; Energy minimizing stuff<br>;<br>emtol =
1000.0<br>emstep = 0.01<br>pbc = xyz<br><br>I included define = -DPOSRE, for restraining the atom postion,<br>I used posre.itp which was genertaed by pdb2gmx.<br><br>Have I done it correctly, because after this also many of the beeta sheets have become short, forming loops.<br>I also want to ask what is the meaning of fx fy and fz :<br><br>; atom type fx fy fz<br> 1 1 1000 1000 1000<br> 5 1 1000 1000 1000<br> 6 1 1000 1000 1000<br> 7 1 1000 1000
1000<br> 8 1 1000 1000 1000<br> 9 1 1000 1000 1000<br> 11 1 1000 1000 1000<br> 12 1 1000 1000 1000<br> 15 1 1000 1000 1000<br> 18 1 1000 1000 1000<br> 19 1 1000 1000 1000<br> 20 1 1000 1000 1000<br> 21 1 1000 1000 1000<br> 22 1 1000 1000 1000<br> 23 1 1000 1000 1000<br><br>which is there in
posre.itp file, and if these should have value of 1000 1000 1000 each ?<br><br>Thanks in advance.<br><div>--<br>Sonali Dhindwal</div><br><br>--- On <b>Wed, 19/5/10, Gaurav Goel <i><gauravgoeluta@gmail.com></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: Gaurav Goel <gauravgoeluta@gmail.com><br>Subject: Re: [gmx-users] enegry minimisation<br>To: "sonali dhindwal" <sonali11dhindwal@yahoo.co.in><br>Date: Wednesday, 19 May, 2010, 8:39 PM<br><br><div id="yiv682528037">For position restraints you need to do the following:<br><br>1. define a name.itp file which looks like:<br><br>; In this topology include file, you will find position restraint<br>; entries for all the heavy atoms in your original pdb file.<br>
; This means that all the protons which were added by pdb2gmx are<br>; not restrained.<br><br>[ position_restraints ]<br>; atom type fx fy fz<br> 1 1 1000 1000 1000<br> 5 1 1000 1000 1000<br>
6 1 1000 1000 1000<br>.......<br>.......<br>_____<br>1,5,6 etc. are the atom indices you want to restrain. section 4.3.1 in manual.<br><br>2. Add "define = -Dname" to your mdp file<br>
<br>3. Add following lines to your topology file<br>; Include Position restraint file<br>#ifdef name<br>#include "name.itp"<br>#endif<br><br>4. compile and run.<br><br>I'm sure you will find mroe information on position-restrain simulation on gmx-users archive.<br>
<br>-Gaurav<br><br><div class="gmail_quote">On Wed, May 19, 2010 at 10:26 AM, sonali dhindwal <span dir="ltr"><<a rel="nofollow" ymailto="mailto:sonali11dhindwal@yahoo.co.in" target="_blank" href="/mc/compose?to=sonali11dhindwal@yahoo.co.in">sonali11dhindwal@yahoo.co.in</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="font-family: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; font-size: inherit; line-height: inherit; font-size-adjust: inherit; font-stretch: inherit;" valign="top">
Hello Gaurav,<br>Can you please help me in suggesting where should I look for providing parameters to constrain the protein backbone and then do EM and then how to run a short MD simulation by constraining the protein backbone.<br>
Sorry to bother you, but as I am new to Gromacs, your help will be highly appreciable.<br>Thanks in advance<br><br><div>--<br>Sonali Dhindwal</div><br><br>--- On <b>Wed, 19/5/10, Gaurav Goel <i><<a rel="nofollow" ymailto="mailto:gauravgoeluta@gmail.com" target="_blank" href="/mc/compose?to=gauravgoeluta@gmail.com">gauravgoeluta@gmail.com</a>></i></b> wrote:<br>
<blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: Gaurav Goel <<a rel="nofollow" ymailto="mailto:gauravgoeluta@gmail.com" target="_blank" href="/mc/compose?to=gauravgoeluta@gmail.com">gauravgoeluta@gmail.com</a>><div class="im">
<br>Subject: Re: [gmx-users] enegry minimisation<br>To: "Discussion list for GROMACS users" <<a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br></div>Date: Wednesday, 19 May, 2010, 6:44 PM<div>
<div></div><div class="h5"><br><br><div>After adding water you can do energy minimization
(EM) in two steps:<br><br>1. Constrain the protein backbone and do EM.<br>2. Now do EM on the full system.<br>3. Run a short MD simulation by constraining the protein backbone.<br>
The above three steps will help hydrate the protein molecule with minimal distortion of protein structure.<br><br>4. Now run a MD on full system.<br><br>for details looks here:<br><a rel="nofollow" target="_blank" href="http://www.google.com/url?sa=t&source=web&ct=res&cd=2&ved=0CBcQFjAB&url=http%3A%2F%2Feugen.leitl.org%2Fchem%2Fkerrigje%2Fpdf_files%2Ffwspidr_tutor.pdf&ei=jOPzS8a3Lab2MdX1_aAO&usg=AFQjCNGB_3mXSQRHuqehBSHXsRyXP1Gymg&sig2=bY3NqXHmruR7eSLVyAuCHQ">http://www.google.com/url?sa=t&source=web&ct=res&cd=2&ved=0CBcQFjAB&url=http%3A%2F%2Feugen.leitl.org%2Fchem%2Fkerrigje%2Fpdf_files%2Ffwspidr_tutor.pdf&ei=jOPzS8a3Lab2MdX1_aAO&usg=AFQjCNGB_3mXSQRHuqehBSHXsRyXP1Gymg&sig2=bY3NqXHmruR7eSLVyAuCHQ</a><br>
<br>-Gaurav<br><br><div class="gmail_quote">On Wed, May 19, 2010 at 8:18 AM, sonali dhindwal <span dir="ltr"><<a rel="nofollow" target="_blank" href="http://mc/compose?to=sonali11dhindwal@yahoo.co.in">sonali11dhindwal@yahoo.co.in</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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Sorry, but I couldnt get your question,<br>I have used this .mdp file for energy minimisation after addition of water and using <pre style="margin: 0em;">GROMOS96 43a1 force field :</pre><br>title = drg_trp<br>
cpp = /lib/cpp ; location of cpp on SGI<br>define = -DFLEX_SPC ; Use Ferguson’s Flexible water model [4]<br>constraints = none<br>integrator = steep<br>dt = 0.002 ; ps !<br>
nsteps =
2000<br>nstlist = 10<br>ns_type = grid<br>rlist = 0.9<br>coulombtype = PME ; Use particle-mesh ewald<br>rcoulomb = 0.9<br>rvdw = 1.0<br>fourierspacing = 0.12<br>fourier_nx = 0<br>
fourier_ny = 0<br>fourier_nz = 0<br>pme_order = 4<br>ewald_rtol = 1e-5<br>optimize_fft = yes<br>;<br>; Energy minimizing stuff<br>;<br>emtol =
1000.0<br>emstep = 0.01<br><br>I hope it will help you to guide me further<br>Thanks<br><div>--<br>Sonali Dhindwal</div><br><br>--- On <b>Wed, 19/5/10, Erik Marklund <i><<a rel="nofollow" target="_blank" href="http://mc/compose?to=erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a>></i></b> wrote:<br>
<blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: Erik Marklund <<a rel="nofollow" target="_blank" href="http://mc/compose?to=erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a>><br>
Subject: Re: [gmx-users] enegry minimisation<br>
To: "Discussion list for GROMACS users" <<a rel="nofollow" target="_blank" href="http://mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Date: Wednesday, 19 May, 2010, 5:31 PM<div><div></div>
<div><br><br><div>
sonali dhindwal skrev:<br>> Hello All<br>> This question may sound trivial to many, but as i am new to this field, please help.<br>> I want to ask a question regarding my previous query of distortion of protein strucutre after molecular dynamcs simulation.<br>
> I have noticed that after enegry minimisation using
steepest decent algorithm, using emtol of 1000 kJ mol^-1 nm^-1 , large amount of distortion occurs.<br>> So is it necessary to do enegry minimisation step before MD, because this is my modeled protein, and i have already done energy minimisation using different program and after that I have done refinement also.<br>
> Thanks and regards<br>> ^<br>> <br>> <br>> --<br>> Sonali Dhindwal<br>> <br>> <br>So how has your system setup changed since your previous EM? Addition of water? Cutoffs? PME?<br><br>-- -----------------------------------------------<br>
Erik Marklund, PhD student<br>Dept. of Cell and Molecular Biology, Uppsala University.<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: +46 18 471 4537 fax: +46 18 511 755<br><a rel="nofollow" target="_blank" href="http://mc/compose?to=erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a> <a rel="nofollow" target="_blank" href="http://folding.bmc.uu.se/">http://folding.bmc.uu.se/</a><br>
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