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

Justin A. Lemkul Thu, 06 May 2010 04:28:05 -0700


xi zhao wrote:

in fact, using Maritni coarse-grained force field in gromacs,corresponding top file is system top file,and gro file is onlycoordinates file for protein. I do not know what the file format fortop2psf.pl in coarse-graind simulation!

Within your system topology, you have to have #included the coarse-grain .itpfile for your protein somewhere. I presume that's what "3ehz.itp" is. That isthe input that top2psf.pl expects. It needs to know the bonds that are in yourCG 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>


--- *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>>
     >
     > --- *10年5月6日，周四, 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: "Gromacs Users' List" <gmx-users@gromacs.org
    <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@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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><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 /<jalem...@vt.edu
    <http://cn.mc151.mail.yahoo.com/mc/compose?to=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>
     >     <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: "Gromacs Users' List" <gmx-users@gromacs.org
    <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org>

><http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@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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     >      >      >
     >      >      > --- *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>
     >     <http://cn.mc151.mail.yahoo.com/mc/compose?to=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>
     >     <http://cn.mc151.mail.yahoo.com/mc/compose?to=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>

><http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@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

> > ><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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     >      >      >      >
     >      >      >      >
     >      >      >      >
     >      >      >     -- ========================================
     >      >      >
     >      >      >     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
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     >     Justin A. Lemkul
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     >     Virginia Tech
     >     Blacksburg, VA
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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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Re: [gmx-users] how to show structure results in Martini coarse-grained simulation?

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