[gmx-users] how to show structure results in Martini coarse-grained simulation?
Justin A. Lemkul
jalemkul at vt.edu
Thu May 6 14:13:24 CEST 2010
xi zhao wrote:
> thank you for your suggestion!
> using 3ehz.itp as in input file, the script produced psf, but how to
> show structure corresponding for the particular time. I do not
> know using of NAMD or charmm file format ?
Load a .pdb file into VMD, then load the .psf file as data into it.
-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,下午7:24
>
>
>
> xi zhao wrote:
> >
> > in fact, using Maritni coarse-grained force field in gromacs,
> corresponding top file is system top file,and gro file is only
> coordinates file for protein. I do not know what the file format for
> top2psf.pl in coarse-graind simulation!
>
> Within your system topology, you have to have #included the
> coarse-grain .itp file for your protein somewhere. I presume that's
> what "3ehz.itp" is. That is the input that top2psf.pl expects. It
> needs to know the bonds that are in your CG structure, information
> contained in your protein's topology.
>
> -Justin
>
> > thank you!
> >
> > 4
> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
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> >
> > --- *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10:59
> >
> >
> >
> > 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
> <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>>>
> > >
> > > --- *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>
> >
> <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: "Gromacs Users' 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>>
> > > 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
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> >
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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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> > > >
> > > > --- *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>
> > <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>
> > >
> <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>
> >
> <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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> >
> <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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> > > >
> <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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> > > > >
> > > > > --- *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>
> > >
> <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>
> > >
> <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>
> > >
> <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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> >
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> > >
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> >
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> > > >
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> >
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> > >
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> >
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> > > > >
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> >
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> > >
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> >
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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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> >
> >
>
> -- ========================================
>
> 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
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
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> 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
========================================
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