[gmx-users] InflateGRO and pentamer protein simulation
shayamra at post.tau.ac.il
shayamra at post.tau.ac.il
Sun Apr 11 16:01:30 CEST 2010
Dear Xi Zhao,
For inserting protein into membrane you might like to try use
g_membed
(link http://wwwuser.gwdg.de/~ggroenh/membed.html)
This is not strictly (yet) a gromacs package, but it can be very
easily be complied and used per instructions of the authors.
Technically, the package 'compress' the protein to be a linear line,
then inserts it into the membrane and starts 'pumping' it back to the
original size.
Hope that help,
-Shay
Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
>
>
> xi zhao wrote:
>> I would like to run a simulation of a pentamers in a POPC membrane,
>> and using new inflategro with doughnut mode, but I have met
>> similar result as the links
>> http://lists.gromacs.org/pipermail/gmx-users/2010-January/047977.html ,I
>> also
>> <http://lists.gromacs.org/pipermail/gmx-users/2010-January/047977.html ,I
>> also> got a lot of errors about uninitialized values. When the
>> script finishes, the membrane is rescaled, but the protein is
>> untouched in the corner of the new box. Please give me some
>> suggestions! Thank you in advance!
>> > best regards!
>
> I think the problem comes from pattern matching in the script. With
> large bilayers, the atom names and numbers will not be split
> correctly; this could be causing a problem for you. I'd again
> suggest that you contact the developer of the program and discuss
> this issue, as it is not really a Gromacs problem and only a few
> people on this list really use such programs. I think you'll find a
> resolution faster that way.
>
> -Justin
>
>>
>>
>>
>> 4
>> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
>>
>> --- *10年4月9日，周五, Justin A. Lemkul /<jalemkul at vt.edu>/* 写道：
>>
>>
>> 发件人: Justin A. Lemkul <jalemkul at vt.edu>
>> 主题: Re: [gmx-users] InflateGRO and pentamer protein simulation
>> 收件人: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>> 日期: 2010年4月9日,周五,上午2:14
>>
>>
>>
>> xi zhao wrote:
>> >
>> >
>> > Dear sir :
>> > I want to a pentamer membrane protein, when I used InflateGRO.pl
>> with /DOUGHNUT Mode, the results were wrong, please help me! /
>>
>> If you want any useful help, you'll have to do a whole lot better
>> than simply saying "the results were wrong." No one on this list
>> will have any idea what you mean. If you believe there is some
>> error in the script itself, you're better off contacting its author.
>>
>> -Justin
>>
>> > 4
>>
>> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>>
>> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>>show
>> " [user at localhost protein-tutorial]$ perl inflategro.txt kkr.gro 4
>> POPC 14 kk_inflated.gro 5 area.dat doughnut protein_subunits
>> > Doughnut mode activated. Protein coordinates will be translated
>> by subunit ....
>> > Reading.....
>> > Reading chain identifiers....
>> > Subunit 1: atom 1 to atom 3238
>> > Subunit 2: atom 3239 to atom 6476
>> > Subunit 3: atom 6477 to atom 9714
>> > Subunit 4: atom 9715 to atom 12952
>> > Subunit 5: atom 12953 to atom 16190
>> > There are 5 protein subunits....
>> > Scaling lipids....
>> > There are 512 lipids...
>> > with 65 atoms per lipid..
>> > Determining upper and lower leaflet...
>> > 256 lipids in the upper...
>> > 256 lipids in the lower leaflet
>> > Checking for overlap....
>> > ...this might actually take a while...
>> > .......
>> > Argument "N4" isn't numeric in printf at inflategro.txt line 708,
>> <CHAINS> line 5.
>> > Argument "C5" isn't numeric in printf at inflategro.txt line 708,
>> <CHAINS> line 5.
>> > Argument "C6" isn't numeric in printf at inflategro.txt line 708,
>> <CHAINS> line 5.
>> > Argument "O7" isn't numeric in printf at inflategro.txt line 708,
>> <CHAINS> line 5.
>> > Argument "P8" isn't numeric in printf at inflategro.txt line 708,
>> <CHAINS> line 5.
>> > Argument "O9" isn't numeric in printf at inflategro.txt line 708,
>> <CHAINS> line 5.
>> > Argument "A1" isn't numeric in printf at inflategro.txt line 708,
>> <CHAINS> line 5.
>> > Argument "A2" isn't numeric in printf at inflategro.txt line 708,
>> <CHAINS> line 5.
>> > Argument "C1" isn't numeric in printf at inflategro.txt line 708,
>> <CHAINS> line 5.
>> > Argument "C2" isn't numeric in printf at inflategro.txt line 708,
>> <CHAINS> line 5.
>> > Argument "C3" isn't numeric in printf at inflategro.txt line 708,
>> <CHAINS> line 5.
>> > Argument "N4" isn't numeric in printf at inflategro.txt line 708,
>> <CHAINS> line 5.
>> > Argument "C5" isn't numeric in printf at inflategro.txt line 708,
>> <CHAINS> line 5.
>> > Argument "C6" isn't numeric in printf at inflategro.txt line 708,
>> <CHAINS> line 5.
>> > Argument "O7" isn't numeric in printf at inflategro.txt line 708,
>> <CHAINS> line 5.
>> > Argument "P8" isn't numeric in printf at inflategro.txt line 708,
>> <CHAINS> line 5.
>> > Argument "O9" isn't numeric in printf at inflategro.txt line 708,
>> <CHAINS> line 5.
>> > Argument "A1" isn't numeric in printf at inflategro.txt line 708,
>> <CHAINS> line 5.
>> > Argument "A2" isn't numeric in printf at inflategro.txt line 708,
>> <CHAINS> line 5.
>> > Calculating Area per lipid...
>> > Protein X-min/max: 23 105
>> > Protein Y-min/max: 18 100
>> > X-range: 82 A Y-range: 82 A
>> > Building 82 X 82 2D grid on protein coordinates...
>> > Calculating area occupied by protein..
>> > full TMD..
>> > upper TMD....
>> > lower TMD....
>> > Area per protein: 49 nm^2
>> > Area per lipid: 9.83158146861789 nm^2
>> > Area per protein, upper half: 38.75 nm^2
>> > Area per lipid, upper leaflet : 9.79362516645161 nm^2
>> > Area per protein, lower half: 45.75 nm^2
>> > Area per lipid, lower leaflet : 9.92548787409836 nm^2
>> > Writing Area per lipid...
>> > Done!
>> >
>> >
>> > -- ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> 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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>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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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