[gmx-users] Re: Inflategro for Coarse Grained
sunny mishra
mishra.sunny at gmail.com
Thu Oct 29 22:39:14 CET 2009
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.
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 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.
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> 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>> 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>>> 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>>
>> <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> | (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
>>
>> ========================================
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
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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
>>
>> ========================================
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
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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
>
> ========================================
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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