Respected Sir,<br><br>Greetings from Pawan.<br>Thanks for your reply.<br>I used to do genbox first and then Inflategro all the time.<br>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 ?<br>
Is it fine if I generate the .gro files using editconf command ?<br>Thanks for your kind help.<br><br>Thanking you,<br>Pawan<br><br><div class="gmail_quote">On Mon, Mar 23, 2009 at 5:02 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im"><br>
<br>
Pawan Kumar wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Respected Sir,<br>
<br>
Greetings from Pawan.<br>
Thanks for your mail.<br>
I will tell you in detail.<br>
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.<br>
Then after inserting the protein with genbox the whole system minimized with an emtol value of 2250.<br>
Then I am trying to do position restraint mdrun where I am getting errors.<br>
Inflategro can be used only after inserting the protein right (which I did using genbox with -vdwd option as 0.6) ?<br>
<br>
</blockquote>
<br></div>
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.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Thanking you,<br>
Pawan<div class="im"><br>
<br>
On Mon, Mar 23, 2009 at 4:39 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Pawan Kumar wrote:<br>
<br>
Hello Justin Sir,<br>
<br></div><div><div></div><div class="h5">
Greetings from Pawan.<br>
Sorry for the inconvenience.<br>
Next time I will keep in mind about the subject line.<br>
I tried deleting those particular atoms where it gave the<br>
maximum force.<br>
<br>
<br>
You said that this atom was part of a lipid. Deleting these atoms<br>
will give you a broken structure and an unrealistic system. It<br>
should also cause grompp to complain.<br>
<br>
<br>
But every time a new atom with a maximum force was given in the<br>
output.<br>
Is it fine to use to use "constraints = all-angles" in order to<br>
overcome the Lincs warnings ?<br>
<br>
<br>
No. LINCS warnings indicate that there is something fundamentally<br>
wrong with your system. It likely stems from how you inserted your<br>
protein into the lipids. Think about it. Your control lipid<br>
bilayer minimized fine. Your protein-membrane system does not, if<br>
that is what we're still talking about. That indicates to me that<br>
the problem is not with the lipids, the problem is with the<br>
insertion of the protein.<br>
<br>
Instead of genbox (which is somewhat crude), try the InflateGRO<br>
script from Tieleman's site. I have used it many times to build<br>
nicely-packed membrane protein systems. It takes substantially<br>
longer to build the system than with genbox, but I think the results<br>
are more reliable.<br>
<br>
-Justin<br>
<br>
Thanks in advance.<br>
<br>
Thanking you,<br>
Pawan<br>
<br>
<br>
<br>
<br>
On Mon, Mar 23, 2009 at 4:16 PM, Justin A. Lemkul<br>
<<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br></div></div><div><div></div><div class="h5">
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>> wrote:<br>
<br>
<br>
When replying to digests, please change the subject line to<br>
something relevant.<br>
<br>
Pawan Kumar wrote:<br>
<br>
Hello Justin Sir,<br>
<br>
Greetings from Pawan.<br>
Sorry for the late reply.<br>
The max. force was 1.2447973e+o5 on atom 19448.<br>
<br>
<br>
An Fmax that high is sure to generate problems. It is up to<br>
you to<br>
inspect your system, understand which atoms are interacting<br>
to cause<br>
such a force, and determine if you've done something wrong.<br>
<br>
-Justin<br>
<br>
This particular atom belongs to one of the lipid residues<br>
of the<br>
bilayer.<br>
I get Lincs warnings whenever I run the position<br>
restraint mdrun.<br>
<br>
Thanking you,<br>
Pawan<br>
<br>
<br>
On Sat, Mar 21, 2009 at 6:08 PM, Justin A. Lemkul<br>
<<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>><br>
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>>> wrote:<br>
<br>
<br>
<br>
Pawan Kumar wrote:<br>
<br>
Hello Justin Sir,<br>
<br>
Greetings from Pawan<br>
Thanks for your valuable suggestion and reply.<br>
Initially I gave the emtol of 1000 and the output<br>
I got was :<br>
Steepest Descents converged to machine precision<br>
in 163 steps<br>
but did not reach the requested Fmax<1000.<br>
Potential Energy = - 4.4516497e+05<br>
<br>
<br>
...and how close did Fmax get to 1000?<br>
<br>
<br>
Even I tried to minimize the popc bilayer which I<br>
took from<br>
Tieleman sir's website ( before generating a<br>
bigger bilayer<br>
using genconf ) but that also converged to machine<br>
precision but<br>
not to the requested Fmax<1000. How do I proceed<br>
further ?<br>
<br>
<br>
Well, these things are not absolute; Fmax = 1000 is<br>
kind of a<br>
rule<br>
of thumb that I use in my own work, but sometimes it<br>
is not<br>
necessary. Careful equilibration should massage your<br>
system into<br>
cooperating.<br>
<br>
-Justin<br>
<br>
Thanks for your suggestions and help.<br>
<br>
Thanking you,<br>
Pawan<br>
<br>
On Thu, Mar 19, 2009 at 9:13 PM,<br>
<br>
Pawan Kumar wrote:<br>
> Hello Justin Sir,<br>
><br>
> Greetings from Pawan<br>
> Thanks for your valuable suggestion and reply.<br>
> After inserting the protein in the bilayer using<br>
genbox I have<br>
minimized<br>
> the whole system without using any position<br>
restraints<br>
(i.e. define =<br>
> -DFLEXIBLE in em.mdp file). I used vanderwaal's<br>
distance<br>
parameter (<br>
> -vdwd of 0.6 ) in the genbox step.<br>
> After running mdrun for energy minimization<br>
I got the<br>
output as :<br>
> Steepest Descents converged to Fmax<2250 in<br>
14 steps.<br>
> Potential energy = - 6.9484700e+05<br>
> Maximum force = 2.2114819e+03 on atom 34277<br>
> Norm. of force = 5.0103039e+04<br>
><br>
<br>
You should try for an Fmax of no greater than 1000.<br>
2250 is<br>
still<br>
very high.<br>
<br>
> I tried decreasing the emtol value in the em.mdp<br>
file but it<br>
ended with<br>
> machine precision.<br>
<br>
How far did it converge? What was Fmax?<br>
<br>
> I have read in literature that 5000 steps of<br>
Steetest<br>
Descents run is<br>
> required after inserting the protein in the<br>
bilayer<br>
which<br>
should be<br>
> followed by atleast 1000 steps of conjugate<br>
gradients. How<br>
can I<br>
> accomplish this ? Is there any parameter to be<br>
given in the<br>
em.mdp file<br>
> ? I use steep as the integrator in the mdp<br>
file for<br>
energy<br>
minimization.<br>
<br>
Read the manual.<br>
<br>
Whether or not that exact setup is going to be<br>
"required" is<br>
likely<br>
system-specific. I would say that as long as<br>
your system<br>
converges<br>
to a stable,<br>
negative Epot with a reasonable Fmax (less than<br>
1000,<br>
but ideally<br>
lower) then<br>
you *may* have an appropriate starting structure.<br>
<br>
-Justin<br>
<br>
> Please help with some suggestions.<br>
> Thanks in advance.<br>
><br>
> Thanking you,<br>
> Pawan<br>
><br>
><br>
><br>
<br>
<br>
<br>
------------------------------------------------------------------------<br>
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<br>
-- <br>
========================================<br>
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ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
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