[gmx-users] Re: Doubt regarding membrane protein in POPC bilayer
Justin A. Lemkul
jalemkul at vt.edu
Mon Mar 23 13:06:10 CET 2009
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 <jalemkul at vt.edu
> <mailto:jalemkul at 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
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at 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
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at 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
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at 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
>
> ========================================
>
>
>
> --
> ========================================
>
> Justin A. Lemkul
> 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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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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