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

Justin A. Lemkul jalemkul at vt.edu
Mon Apr 12 15:25:56 CEST 2010



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

Then surely you made some sort of modification to the inflategro.pl script in 
order to make it work with a CG structure, right?  The standard script matches 
C-alpha and P positions to do scaling of coordinates, but MARTINI nomenclature 
will not match, at least in the case of the protein.  If you haven't made any 
modifications, perhaps that is the problem as well :)

-Justin

> 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: "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
>     <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
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>>/* 写道:
>      >
>      >
>      >     发件人: Justin A. Lemkul <jalemkul at vt.edu
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@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
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@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>
>      > 
>        <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
>      >
>      >     ========================================
>      >     -- gmx-users mailing list    gmx-users at gromacs.org
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>
>      > 
>        <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>
>      >     http://lists.gromacs.org/mailman/listinfo/gmx-users
>      >     Please search the archive at http://www.gromacs.org/search before
>      >     posting!
>      >     Please don't post (un)subscribe requests to the list. Use the www
>      >     interface or send it to gmx-users-request at gromacs.org
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org>
>      > 
>        <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org>.
>      >     Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>      >
>      >
>      > 
> 
>     -- ========================================
> 
>     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
> 
>     ========================================
>     -- gmx-users mailing list    gmx-users at gromacs.org
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>
>     http://lists.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at http://www.gromacs.org/search before
>     posting!
>     Please don't post (un)subscribe requests to the list. Use the www
>     interface or send it to gmx-users-request at gromacs.org
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org>.
>     Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
>  

-- 
========================================

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

========================================



More information about the gromacs.org_gmx-users mailing list