xi zhao wrote:
in fact, how to deal with format problem in coarse-grained ?
What do you mean?
-Justin
thank you!
4
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--- *10年5月6日，周四, Justin A. Lemkul /<jalem...@vt.edu>/* 写道：
发件人: Justin A. Lemkul <jalem...@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@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
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> --- *10年5月3日，周一, Justin A. Lemkul /<jalem...@vt.edu
<http://cn.mc151.mail.yahoo.com/mc/compose?to=jalem...@vt.edu>>/* 写道：
>
>
> 发件人: Justin A. Lemkul <jalem...@vt.edu
<http://cn.mc151.mail.yahoo.com/mc/compose?to=jalem...@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@gromacs.org
<http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@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
>
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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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