[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
> <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
> <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
> <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://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>
> > >
> <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://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