--
Sonali Dhindwal
--- On *Thu, 20/5/10, Gaurav Goel /<gauravgoel...@gmail.com>/* wrote:
From: Gaurav Goel <gauravgoel...@gmail.com>
Subject: Re: [gmx-users] enegry minimisation
To: jalem...@vt.edu, "Discussion list for GROMACS users"
<gmx-users@gromacs.org>
Date: Thursday, 20 May, 2010, 5:36 PM
Can you try using g_rms to compare the difference between the
structures before and after EM.
-Gaurav
On Thu, May 20, 2010 at 7:53 AM, Justin A. Lemkul <jalem...@vt.edu
</mc/compose?to=jalem...@vt.edu>> wrote:
>
>
> sonali dhindwal wrote:
>>
>> Hello Gaurav,
>> Thanks for your reply,
>> I did position restrained enegry minimisation, and used
following .mdp
>> file for the same
>>
>> title = protein
>> cpp = /usr/bin/cpp ; the c pre-processor
>> define = -DPOSRE
>> constraints = none
>> integrator = steep
>> dt = 0.002 ; ps !
>> nsteps = 1000
>> nstlist = 10
>> ns_type = grid
>> rlist = 0.9
>> coulombtype = PME
>> rcoulomb = 0.9
>> rvdw = 0.9
>> fourierspacing = 0.12
>> fourier_nx = 0
>> fourier_ny = 0
>> fourier_nz = 0
>> pme_order = 4
>> ewald_rtol = 1e-5
>> optimize_fft = yes
>> ;
>> ; Energy minimizing stuff
>> ;
>> emtol = 1000.0
>> emstep = 0.01
>> pbc = xyz
>>
>> I included define = -DPOSRE, for restraining the atom postion,
>> I used posre.itp which was genertaed by pdb2gmx.
>>
>> Have I done it correctly, because after this also many of the
beeta sheets
>> have become short, forming loops.
>
> Well, you haven't properly defined position restraints. The default
> (produced by pdb2gmx) requires "define = -DPOSRES" not "-DPOSRE."
If you
> have for some reason modified the topology, then maybe your
approach is
> correct, but otherwise your position restraints are not being
applied.
>
> I also find it very curious that such substantial changes are
taking place
> during a simple energy minimization. Are you sure the effects you are
> seeing are not simply due to the visualization software you are using
> guessing the incorrect secondary structure type? I have had that
experience
> numerous times, especially in the case of beta-strands. DSSP
tells me that,
> geometrically, I have beta-strands, but the visualization
software renders
> coil structures.
>
> In any case, large structural deviations during EM suggest something
> fundamentally wrong with the model. Usually the changes in EM are
small,
> since it is performed at 0 K. Only huge forces would cause any
sort of
> structural change.
>
>> I also want to ask what is the meaning of fx fy and fz :
>>
>
> Force constants (kJ mol^-1 nm^-2) in the x, y, and z directions.
>
>> ; atom type fx fy fz
>> 1 1 1000 1000 1000
>> 5 1 1000 1000 1000
>> 6 1 1000 1000 1000
>> 7 1 1000 1000 1000
>> 8 1 1000 1000 1000
>> 9 1 1000 1000 1000
>> 11 1 1000 1000 1000
>> 12 1 1000 1000 1000
>> 15 1 1000 1000 1000
>> 18 1 1000 1000 1000
>> 19 1 1000 1000 1000
>> 20 1 1000 1000 1000
>> 21 1 1000 1000 1000
>> 22 1 1000 1000 1000
>> 23 1 1000 1000 1000
>>
>> which is there in posre.itp file, and if these should have value
of 1000
>> 1000 1000 each ?
>>
>
> These default values are typically quite sufficient to restrain the
> structure.
>
> -Justin
>
>> Thanks in advance.
>> --
>> Sonali Dhindwal
>>
>>
>> --- On *Wed, 19/5/10, Gaurav Goel /<gauravgoel...@gmail.com
</mc/compose?to=gauravgoel...@gmail.com>>/* wrote:
>>
>>
>> From: Gaurav Goel <gauravgoel...@gmail.com
</mc/compose?to=gauravgoel...@gmail.com>>
>> Subject: Re: [gmx-users] enegry minimisation
>> To: "sonali dhindwal" <sonali11dhind...@yahoo.co.in
</mc/compose?to=sonali11dhind...@yahoo.co.in>>
>> Date: Wednesday, 19 May, 2010, 8:39 PM
>>
>> For position restraints you need to do the following:
>>
>> 1. define a name.itp file which looks like:
>>
>> ; In this topology include file, you will find position restraint
>> ; entries for all the heavy atoms in your original pdb file.
>> ; This means that all the protons which were added by pdb2gmx are
>> ; not restrained.
>>
>> [ position_restraints ]
>> ; atom type fx fy fz
>> 1 1 1000 1000 1000
>> 5 1 1000 1000 1000
>> 6 1 1000 1000 1000
>> .......
>> .......
>> _____
>> 1,5,6 etc. are the atom indices you want to restrain. section 4.3.1
>> in manual.
>>
>> 2. Add "define = -Dname" to your mdp file
>>
>> 3. Add following lines to your topology file
>> ; Include Position restraint file
>> #ifdef name
>> #include "name.itp"
>> #endif
>>
>> 4. compile and run.
>>
>> I'm sure you will find mroe information on position-restrain
>> simulation on gmx-users archive.
>>
>> -Gaurav
>>
>> On Wed, May 19, 2010 at 10:26 AM, sonali dhindwal
>> <sonali11dhind...@yahoo.co.in
</mc/compose?to=sonali11dhind...@yahoo.co.in>
>> </mc/compose?to=sonali11dhind...@yahoo.co.in
</mc/compose?to=sonali11dhind...@yahoo.co.in>>> wrote:
>>
>> Hello Gaurav,
>> 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.
>> Sorry to bother you, but as I am new to Gromacs, your help will
>> be highly appreciable.
>> Thanks in advance
>>
>> --
>> Sonali Dhindwal
>>
>>
>> --- On *Wed, 19/5/10, Gaurav Goel /<gauravgoel...@gmail.com
</mc/compose?to=gauravgoel...@gmail.com>
>> </mc/compose?to=gauravgoel...@gmail.com
</mc/compose?to=gauravgoel...@gmail.com>>>/* wrote:
>>
>>
>> From: Gaurav Goel <gauravgoel...@gmail.com
</mc/compose?to=gauravgoel...@gmail.com>
>> </mc/compose?to=gauravgoel...@gmail.com
</mc/compose?to=gauravgoel...@gmail.com>>>
>>
>> Subject: Re: [gmx-users] enegry minimisation
>> To: "Discussion list for GROMACS users"
>> <gmx-users@gromacs.org </mc/compose?to=gmx-us...@gromacs.org>
</mc/compose?to=gmx-us...@gromacs.org
</mc/compose?to=gmx-us...@gromacs.org>>>
>> Date: Wednesday, 19 May, 2010, 6:44 PM
>>
>>
>> After adding water you can do energy minimization (EM) in
>> two steps:
>>
>> 1. Constrain the protein backbone and do EM.
>> 2. Now do EM on the full system.
>> 3. Run a short MD simulation by constraining the protein
>> backbone.
>> The above three steps will help hydrate the protein molecule
>> with minimal distortion of protein structure.
>>
>> 4. Now run a MD on full system.
>>
>> for details looks here:
>>
>>
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>
>>
>>
<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>>
>>
>> -Gaurav
>>
>> On Wed, May 19, 2010 at 8:18 AM, sonali dhindwal
>> <sonali11dhind...@yahoo.co.in
</mc/compose?to=sonali11dhind...@yahoo.co.in>
>> <http://mc/compose?to=sonali11dhind...@yahoo.co.in>> wrote:
>>
>> Sorry, but I couldnt get your question,
>> I have used this .mdp file for energy minimisation after
>> addition of water and using
>>
>> GROMOS96 43a1 force field :
>>
>>
>> title = drg_trp
>> cpp = /lib/cpp ; location of cpp on SGI
>> define = -DFLEX_SPC ; Use Ferguson’s Flexible water
>> model [4]
>> constraints = none
>> integrator = steep
>> dt = 0.002 ; ps !
>> nsteps = 2000
>> nstlist = 10
>> ns_type = grid
>> rlist = 0.9
>> coulombtype = PME ; Use particle-mesh ewald
>> rcoulomb = 0.9
>> rvdw = 1.0
>> fourierspacing = 0.12
>> fourier_nx = 0
>> fourier_ny = 0
>> fourier_nz = 0
>> pme_order = 4
>> ewald_rtol = 1e-5
>> optimize_fft = yes
>> ;
>> ; Energy minimizing stuff
>> ;
>> emtol = 1000.0
>> emstep = 0.01
>>
>> I hope it will help you to guide me further
>> Thanks
>> --
>> Sonali Dhindwal
>>
>>
>> --- On *Wed, 19/5/10, Erik Marklund
>> /<er...@xray.bmc.uu.se </mc/compose?to=er...@xray.bmc.uu.se>
>> <http://mc/compose?to=er...@xray.bmc.uu.se>>/* wrote:
>>
>>
>> From: Erik Marklund <er...@xray.bmc.uu.se
</mc/compose?to=er...@xray.bmc.uu.se>
>> <http://mc/compose?to=er...@xray.bmc.uu.se>>
>> Subject: Re: [gmx-users] enegry minimisation
>> To: "Discussion list for GROMACS users"
>> <gmx-users@gromacs.org </mc/compose?to=gmx-us...@gromacs.org>
>> <http://mc/compose?to=gmx-us...@gromacs.org>>
>> Date: Wednesday, 19 May, 2010, 5:31 PM
>>
>>
>> sonali dhindwal skrev:
>> > Hello All
>> > This question may sound trivial to many, but as i
>> am new to this field, please help.
>> > I want to ask a question regarding my previous
>> query of distortion of protein strucutre after
>> molecular dynamcs simulation.
>> > 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.
>> > 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.
>> > Thanks and regards
>> > ^
>> >
>> >
>> > --
>> > Sonali Dhindwal
>> >
>> >
>> So how has your system setup changed since your
>> previous EM? Addition of water? Cutoffs? PME?
>>
>> -- -----------------------------------------------
>> Erik Marklund, PhD student
>> Dept. of Cell and Molecular Biology, Uppsala
>> University.
>> Husargatan 3, Box 596, 75124 Uppsala, Sweden
>> phone: +46 18 471 4537 fax: +46 18 511 755
>> er...@xray.bmc.uu.se </mc/compose?to=er...@xray.bmc.uu.se>
>> <http://mc/compose?to=er...@xray.bmc.uu.se>
>> http://folding.bmc.uu.se/
>>
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>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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