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

[xi zhao]

in fact, how to deal with format problem in coarse-grained ?
thank you!




--- 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>
> 
> --- *10年5月3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] how to show structure results in Martini
>     coarse-grained simulation?
>     收件人: "Discussion list for GROMACS users" <gmx-users at 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
>     <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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