[gmx-users] InflateGRO and pentamer protein simulation

xi zhao zhaoxiitc2002 at yahoo.com.cn
Mon Apr 12 02:41:44 CEST 2010 

Dear sir:
Thank you for your help! 




--- 10年4月11日，周日, shayamra at post.tau.ac.il <shayamra at post.tau.ac.il> 写道：


发件人: shayamra at post.tau.ac.il <shayamra at post.tau.ac.il>
主题: Re: [gmx-users] InflateGRO and pentamer protein simulation
收件人: jalemkul at vt.edu, "Discussion list for GROMACS users" <gmx-users at gromacs.org>
日期: 2010年4月11日,周日,下午10:01


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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