[gmx-users] Re: Inflategro for Coarse Grained
Justin A. Lemkul
jalemkul at vt.edu
Thu Oct 29 22:55:51 CET 2009
sunny mishra wrote:
> Ok. I guess that makes sense. If you say I can send you my system.gro
> file (after catting the system as per our recent conversation) and my
> protein.gro and lipid.gro files (In which the protein is inserted before
> our conversation) and if you visualize that in VMD you will get more
> idea of what I am trying to ask? Can I do that?
>
I'm sorry, but no, I don't really have time for extra work right now, nor do I
know anything about the system you're studying. That's your job to justify the
position of the system (and adjust it with editconf -translate, if necessary).
The position should not simply be an aesthetic observation, it should be based
on any experimental data available. And like I said, if it is off slightly from
center, equilibration may help place it correctly. With CG, you should be able
to probe long time frames, over which the system may change quite a bit.
-Justin
>
>
> On Thu, Oct 29, 2009 at 5:46 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> sunny mishra wrote:
>
> Well yes I guess I am getting the same thing what I expected but
> now I am little confused here and I don't know how to explain
> you this but I will try. Initially I aligned my protein using
> TMDET results and centered that at ORIGIN and then I centered
> the lipid at origin using geom_center script provided in VMD and
> when I visualized that, the protein was properly inserted in
> the lipid the way MARTINI folks have shown in their website.
>
>
> I am unfamiliar with either of these programs, but I can tell you
> that if you center a molecule at the coordinate origin, that
> location (0, 0, 0) corresponds to the corner of the box, by GROMACS
> convention. This is probably the root of the problem you were
> seeing. I do not know what the VMD script does. I would think them
> both unnecessary for GROMACS use (at least in this application),
> since all manipulations can easily be done with editconf.
>
>
> After that I followed your tutorial and made the system.gro file
> by catting lipid and protein and its visualization gives me the
> same thing
>
>
> You can't be guaranteed that different procedures will lead to
> compatible alignment, as you have undoubtedly discovered :)
>
>
> as I was getting earlier. Now after that when I run the
> inflategro script for the system.gro file and scale the lipid by
> the factor of 4, the protein goes apart from lipid (I dnt know
> why) and after our recent conversation I did the same thing but
> now the protein is shifted little upwards but still it is at the
> center of lipid. Now I don't know whether this factor will
> matter a lot or not? I hope you got my question.
>
>
> I don't know how you define "shifted upwards" - relative to where
> editconf placed it, or relative to where you want it to be? If it
> is not too far from the center, and the proper positioning is to
> have the center of the protein aligned with the center of the
> bilayer, it may assume this position after some equilibration.
>
> -Justin
>
> In summary, earlier the upper portion of protein was inserted
> fully same as shown in the martini website but after doing the
> inflategro without running EM it shifted little upwards but
> still at the center so I dnt know whether this will matter a lot
> or not?
>
>
>
> On Thu, Oct 29, 2009 at 5:26 PM, Justin A. Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>
>
>
> sunny mishra wrote:
>
> Alright. I have done this....I have made another
> lipid_newbox.gro file and wrote same box vectors as of
> lipid.gro
> file
>
> For LIPID :
>
> editconf -f lipid.gro -o lipid_newbox.gro -c -box 13.29820
> 13.29820 6.59160
>
> For Protein :
>
> editconf -f protein.gro -o protein_newbox.gro -c -box
> 13.29820
> 13.29820 6.59160
>
> Then cat the system and made system.gro file and did
> inflategro
> of the system.gro file. Do you think this is the correct
> way and
> now when I visualize this in VMD the protein is shifted
> little
> upwards but it is at the center of the lipid.
>
>
> Well, did you get what you expected when you ran InflateGRO? The
> protein and lipid should have the same center; that's what the
> editconf commands did, as I've told you. If you need the
> protein to
> be placed differently, you must specify a different center
> (providing the coordinates to editconf -center).
>
> -Justin
>
> Sunny
>
> On Thu, Oct 29, 2009 at 4:59 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:
>
>
>
> sunny mishra wrote:
>
> No. But in order to do that with lipid.gro what
> co-ordinates
> should I have to take?
>
>
> I think you need to differentiate between
> "coordinates" and "box
> vectors." You should center the molecule in the box
> (defined
> by the
> vectors in the last line of the .gro file). I assumed
> you were
> specifying these box vectors with -box.
>
> So, for both the protein and the lipid coordinate
> files, you
> need to use
>
> editconf -c -box (x, y, z from .gro file)
>
> -Justin
>
> On Thu, Oct 29, 2009 at 4:40 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:
>
>
>
> sunny mishra wrote:
>
> okk...here are the commands which I am givng...
>
> editconf -f 1SU4_cleancg_trans.gro -o
> 1SU4_newbox.gro -c -box
> 13.29820 13.29820 6.59160
>
> I get the 1SU4_newbox.gro which has
> co-ordinates
> 13.29820
> 13.29820 6.59160
>
>
> Have you done the same with lipid.gro? If the
> protein and
> the lipid
> are in different coordinate systems (i.e.,
> lipid.gro
> centered
> at the
> origin and protein centered within the box,
> which has
> its corner
> placed at the origin) then you will have a problem.
>
> -Justin
>
> cat 1SU4_newbox.gro lipid.gro > system..gro
>
> Now here system.gro also has co-ordinates
> 13.29820
> 13.29820 6.59160
>
> now inflategro:
>
> inflategro system.gro 4 DSPC 14 -o
> inflated_bilayer.gro 5
>
> Now when i visualize my output file in VMD then
> protein and
> lipid are seperated and even after i scale
> it to
> .95 they dnt
> meet....they are still apart, I was hoping that
> lipid will be
> scaled and protein shud have remained in
> the center of
> the lipid
> but that doesn't happen. I hope you got my
> question
>
> On Thu, Oct 29, 2009 at 4:25 PM, Justin A.
> Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
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> <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 <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:
>
>
>
> sunny mishra wrote:
>
> Yes I did the same and when I see my
> system.gro
> file it
> gives me
> the dimensions of the protein box
> half of
> the lipid
> bilayer box
> so that means it should now be set
> in the
> center
> of the lipid
> bilayer. But after
>
>
> I don't understand what you mean.
>
>
> that when I run the inflategro
> script and
> see my
> output
> file the
> protein and lipid are separated and
> I dnt
> know why?
>
>
> Can you post the actual commands you're
> using?
>
> -Justin
>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> 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>
> <http://vt.edu> | (540)
>
> 231-9080
>
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
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> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> 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
> Ph.D. Candidate
> 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
> Ph.D. Candidate
> 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
> Ph.D. Candidate
> 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
Ph.D. Candidate
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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