[gmx-users] how to show structure results in Martini coarse-grained simulation?

Justin A. Lemkul jalemkul at vt.edu
Thu May 6 04:59:57 CEST 2010



xi zhao wrote:
> produce input file , in coarse grained , no standard protein top file
> 

I still don't understand what your question is.  Are you still having problems 
with top2psf?  If so, please explain what the difficulty is or what exactly 
you're trying to do.

-Justin

> 
> 4 
> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
> 
> --- *10年5月6日,周四, Justin A. Lemkul /<jalemkul at vt.edu>/* 写道:
> 
> 
>     发件人: Justin A. Lemkul <jalemkul at vt.edu>
>     主题: Re: [gmx-users] how to show structure results in Martini
>     coarse-grained simulation?
>     收件人: "Gromacs Users' List" <gmx-users at gromacs.org>
>     日期: 2010年5月6日,周四,上午10:37
> 
> 
> 
>     xi zhao wrote:
>      > in fact, how to deal with format problem in coarse-grained ?
> 
>     What do you mean?
> 
>     -Justin
> 
>      > thank you!
>      >
>      >
>      > 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5月6日,周四, 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] how to show structure results in Martini
>      >     coarse-grained simulation?
>      >     收件人: "Gromacs Users' List" <gmx-users at gromacs.org
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>>
>      >     日期: 2010年5月6日,周四,上午9:40
>      >
>      >
>      >
>      >     xi zhao wrote:
>      >      >
>      >      > Dear Sir :
>      >      > The script require what format for top file? my top file
>     is here:
>      >      >
>      >
>      >     The input is the actual protein topology, not the system
>     topology.
>      >
>      >     -Justin
>      >
>      >      > ;
>      >      > ; Example topology file for MARTINI 2.0
>      >      > ;
>      >      > ; First include the file containing all particle definitions,
>      >      > ; the interaction matrix, plus the topology for water.
>      >      > #include "martini_v2.1.itp"
>      >      > #include "martini_v2.0_ions.itp"
>      >      > #include "martini_v2.0_lipids.itp"
>      >      > #include "3ehz.itp"
>      >      > ; Include Position restraint file
>      >      > #ifdef POSRES
>      >      > #include "s.itp"
>      >      > #endif
>      >      > [ system ]
>      >      > CGprotein  ion channel
>      >      > [ molecules ]
>      >      > ; name  number
>      >      > Protein     1
>      >      > POPC       502
>      >      > W         18934
>      >      > but run top2psf.pl
>      >      > "Cannot open atoms for reading: No such file or directory"
>      >      > please help me!
>      >      > 4
>      > 
>        <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
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>      > 
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>      >      >
>      >      > --- *10年5月3日,周一, Justin A. Lemkul /<jalemkul at vt.edu
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@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>
>      >     <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>>
>      >      >     主题: Re: [gmx-users] how to show structure results in
>     Martini
>      >      >     coarse-grained simulation?
>      >      >     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>
>      > 
>        <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>>
>      >      >     日期: 2010年5月3日,周一,上午8:08
>      >      >
>      >      >
>      >      >
>      >      >     xi zhao wrote:
>      >      >      > Dear user:
>      >      >      > how to show struture or conformation in Martini
>     coarse-grained
>      >      >     simulation, using VMD or other?
>      >      >      > Please give me some suggestion!
>      >      >      > thank you!
>      >      >
>      >      >     What kind of rendering do you want to do?  There are
>     some scripts
>      >      >     linked below to render bonds in a CG structure.
>      >      >
>      >      >       
>     http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD#VMD_and_coarse-grained_simulations
>      >      >
>      >      >     -Justin
>      >      >
>      >      >      >
>      >      >      >
>      >      >      > 4
>      >      >       
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
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>      > 
>        <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
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>      >      >       
>     <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
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>      > 
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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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>      >     -- ========================================
>      >
>      >     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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>  

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

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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