[gmx-users] Doubt regarding membrane protein in POPC bilayer
Pawan Kumar
pawan.chinari at gmail.com
Mon Mar 23 12:20:27 CET 2009
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) ?
Thanking you,
Pawan
On Mon, Mar 23, 2009 at 4:39 PM, Justin A. Lemkul <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>> 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>>> 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> | (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
>>
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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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