[gmx-users] construct CG membrane protein and CG membrane and inflategro.pl

[xi zhao]

Dear Sir : In fact,  these structures were initially centered within the same coordinate system as your Gromacs Tutorials .



--- 10年4月12日，周一, Justin A. Lemkul <jalemkul at vt.edu> 写道：


发件人: Justin A. Lemkul <jalemkul at vt.edu>
主题: Re: [gmx-users] construct CG membrane protein and CG membrane and inflategro.pl
收件人: "Gromacs Users' List" <gmx-users at gromacs.org>
日期: 2010年4月12日,周一,下午9:07




xi zhao wrote:
> 
> my procesure:
> 1. cat cgprotein cgmembrane>system.gro (using Martini force field)

Were these structures initially centered within the same coordinate system?  By your description, it sounds like these two components are simply not placed properly.  There is a membrane protein tutorial linked from the Gromacs Tutorials page that guides you through constructing an atomistic membrane protein system using InflateGRO.  You might find it useful.

-Justin

> 2 perl inflategro.pl system.gro 4 POPC 14 system_inflated.gro 5 area.dat
> 3. grompp_d -f em.mdp -c system_inflated.gro  -p topol.top -o system_inflatedem.tpr (with strong postion restraint)
> 4. mdrun
> 5 in the system_inflatedem.gro , the protein and membrane  separate each other.
> please help me !
>  
> 4 <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
> 
> --- *10年4月12日，周一, Justin A. Lemkul /<jalemkul at vt.edu>/* 写道：
> 
> 
>     发件人: Justin A. Lemkul <jalemkul at vt.edu>
>     主题: Re: [gmx-users] construct CG membrane protein and CG membrane
>     and inflategro.pl
>     收件人: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>     日期: 2010年4月12日,周一,下午8:42
> 
> 
> 
>     xi zhao wrote:
>      >
>      >
>      > Dear Gromacs users:
>      > I use inflateGRO.pl to insert CG protein in to CG POPC membrane,
>     but when carryied EM with Strong POStion REStraint, the protien and
>     membrane were apart. Please help me!
> 
>     What does "apart" mean?  If you want free help, you have to make it
>     easy to help you.  That means thorough descriptions of what you're
>     doing, what you're seeing, and if necessary, posting images online
>     (not as attachments!) for us to take a look.  The InflateGRO method
>     should generate a configuration that has molecules separated by a
>     large amount of space, but if there is something else wrong you'll
>     have to provide a better description.
> 
>     -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>>
>      >
>      >
>      > 
>     -- ========================================
> 
>     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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