Pawan Kumar wrote:
Respected Sir,
Greetings from Pawan.
Thanks for your reply.
I used to do genbox first and then Inflategro all the time.
Is it possible to concatenate one file after the other using " vi
editor" - I mean just copying the contents of the membrane.gro file at
the end of protein.gro file ?
cat protein.gro membrane.gro > system.gro
Is it fine if I generate the .gro files using editconf command ?
Yes, you will have to center the protein and membrane appropriately, within a
box that has the same dimensions.
-Justin
Thanks for your kind help.
Thanking you,
Pawan
On Mon, Mar 23, 2009 at 5:02 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Pawan Kumar wrote:
Respected Sir,
Greetings from Pawan.
Thanks for your mail.
I will tell you in detail.
The control lipid bilayer ( which is generated using genconf
-nbox 2 2 1 -dist 0 0 0 ) minimized fine with an emtol value of
1510.
Then after inserting the protein with genbox the whole system
minimized with an emtol value of 2250.
Then I am trying to do position restraint mdrun where I am
getting errors.
Inflategro can be used only after inserting the protein right
(which I did using genbox with -vdwd option as 0.6) ?
No. Read the documentation carefully. You first concatenate your
protein and membrane .gro files, then use InflateGRO on that system.
There is no genbox involved when using InflateGRO, hence why I
suggested it as a (potentially) more reliable method.
-Justin
Thanking you,
Pawan
On Mon, Mar 23, 2009 at 4:39 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
Pawan Kumar wrote:
Hello Justin Sir,
Greetings from Pawan.
Sorry for the inconvenience.
Next time I will keep in mind about the subject line.
I tried deleting those particular atoms where it gave the
maximum force.
You said that this atom was part of a lipid. Deleting these
atoms
will give you a broken structure and an unrealistic system. It
should also cause grompp to complain.
But every time a new atom with a maximum force was given
in the
output.
Is it fine to use to use "constraints = all-angles" in
order to
overcome the Lincs warnings ?
No. LINCS warnings indicate that there is something
fundamentally
wrong with your system. It likely stems from how you
inserted your
protein into the lipids. Think about it. Your control lipid
bilayer minimized fine. Your protein-membrane system does
not, if
that is what we're still talking about. That indicates to me that
the problem is not with the lipids, the problem is with the
insertion of the protein.
Instead of genbox (which is somewhat crude), try the InflateGRO
script from Tieleman's site. I have used it many times to build
nicely-packed membrane protein systems. It takes substantially
longer to build the system than with genbox, but I think the
results
are more reliable.
-Justin
Thanks in advance.
Thanking you,
Pawan
On Mon, Mar 23, 2009 at 4:16 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>> wrote:
When replying to digests, please change the subject
line to
something relevant.
Pawan Kumar wrote:
Hello Justin Sir,
Greetings from Pawan.
Sorry for the late reply.
The max. force was 1.2447973e+o5 on atom 19448.
An Fmax that high is sure to generate problems. It is
up to
you to
inspect your system, understand which atoms are
interacting
to cause
such a force, and determine if you've done something
wrong.
-Justin
This particular atom belongs to one of the lipid
residues
of the
bilayer.
I get Lincs warnings whenever I run the position
restraint mdrun.
Thanking you,
Pawan
On Sat, Mar 21, 2009 at 6:08 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>>> wrote:
Pawan Kumar wrote:
Hello Justin Sir,
Greetings from Pawan
Thanks for your valuable suggestion and reply.
Initially I gave the emtol of 1000 and the
output
I got was :
Steepest Descents converged to machine
precision
in 163 steps
but did not reach the requested Fmax<1000.
Potential Energy = - 4.4516497e+05
...and how close did Fmax get to 1000?
Even I tried to minimize the popc bilayer
which I
took from
Tieleman sir's website ( before generating a
bigger bilayer
using genconf ) but that also converged to
machine
precision but
not to the requested Fmax<1000. How do I
proceed
further ?
Well, these things are not absolute; Fmax = 1000 is
kind of a
rule
of thumb that I use in my own work, but
sometimes it
is not
necessary. Careful equilibration should
massage your
system into
cooperating.
-Justin
Thanks for your suggestions and help.
Thanking you,
Pawan
On Thu, Mar 19, 2009 at 9:13 PM,
Pawan Kumar wrote:
> Hello Justin Sir,
>
> Greetings from Pawan
> Thanks for your valuable suggestion
and reply.
> After inserting the protein in the
bilayer using
genbox I have
minimized
> the whole system without using any
position
restraints
(i.e. define =
> -DFLEXIBLE in em.mdp file). I used
vanderwaal's
distance
parameter (
> -vdwd of 0.6 ) in the genbox step.
> After running mdrun for energy
minimization
I got the
output as :
> Steepest Descents converged to
Fmax<2250 in
14 steps.
> Potential energy = - 6.9484700e+05
> Maximum force = 2.2114819e+03 on atom
34277
> Norm. of force = 5.0103039e+04
>
You should try for an Fmax of no greater
than 1000.
2250 is
still
very high.
> I tried decreasing the emtol value in
the em.mdp
file but it
ended with
> machine precision.
How far did it converge? What was Fmax?
> I have read in literature that 5000
steps of
Steetest
Descents run is
> required after inserting the protein
in the
bilayer
which
should be
> followed by atleast 1000 steps of
conjugate
gradients. How
can I
> accomplish this ? Is there any
parameter to be
given in the
em.mdp file
> ? I use steep as the integrator in
the mdp
file for
energy
minimization.
Read the manual.
Whether or not that exact setup is going
to be
"required" is
likely
system-specific. I would say that as
long as
your system
converges
to a stable,
negative Epot with a reasonable Fmax
(less than
1000,
but ideally
lower) then
you *may* have an appropriate starting
structure.
-Justin
> Please help with some suggestions.
> Thanks in advance.
>
> Thanking you,
> Pawan
>
>
>
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-- ========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu>
<http://vt.edu> <http://vt.edu>
<http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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-- ========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu>
<http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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-- ========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
========================================
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Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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ICTAS Doctoral Scholar
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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