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>/* wrote:
From: Gaurav Goel <gauravgoel...@gmail.com>
Subject: Re: [gmx-users] enegry minimisation
To: "sonali dhindwal" <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>> 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>>/* wrote:
From: Gaurav Goel <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>>
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>
-Gaurav
On Wed, May 19, 2010 at 8:18 AM, sonali dhindwal
<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
<http://mc/compose?to=er...@xray.bmc.uu.se>>/* wrote:
From: Erik Marklund <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
<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
<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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