[gmx-users] InflateGRO and pentamer protein simulation
Justin A. Lemkul
jalemkul at vt.edu
Fri Apr 9 16:39:33 CEST 2010
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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