[gmx-users] Re: Doubt regarding membrane protein in POPC bilayer

Justin A. Lemkul jalemkul at vt.edu
Mon Mar 23 12:32:36 CET 2009



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>> 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>>> 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>>>> 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> | (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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> 
>     -- 
>     ========================================
> 
>     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
> 
>     ========================================
> 
> 

-- 
========================================

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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