[gmx-users] how to use atom2cg.awk
Justin A. Lemkul
jalemkul at vt.edu
Mon May 11 14:33:10 CEST 2009
xi zhao wrote:
> Dear sir:
> This is my modified script, please see it! I take CG simulations
> according to http://md.chem.rug.nl/marrink/coarsegrain.html.
> Thank you !
>
Then your structure should be built appropriately.
-Justin
>
> 4
> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
>
> --- *09年5月11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 use atom2cg.awk
> 收件人: "Gromacs Users' List" <gmx-users at gromacs.org>
> 日期: 2009年5月11日,周一,下午6:49
>
>
>
> xi zhao wrote:
> > Dear Sir:
> > In fact, I have modified the script as you said, but the CG
> strucrute produced is not different in secondary strucure with
> native PDB structure: CG structure became a line strucrue! Please
> help me! Or give me a good script!
>
> Visualization is not an appropriate method to use to determine the
> validity of your procedure. The CG model will look a bit strange
> when rendered as "lines" in most visualization software. You did
> modify each line of the script, inserting $5 between every $4 and
> $6, correct?
>
> -Justin
>
> > Thank you very much!
> > Best regards!
> >
> > 4
> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
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> >
> > --- *09年5月11日，周一, 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 use atom2cg.awk
> > 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: 2009年5月11日,周一,上午8:22
> >
> >
> >
> > xi zhao wrote:
> > > Dear sir :
> > > how to motify the $5 in details?
> > > Thank you!
> > >
> >
> > Use a text editor (vi, emacs, gedit, etc), like you would to
> create
> > any script.
> >
> > -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>
> >
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> > >
> > > --- *09年5月8日，周五, 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 use atom2cg.awk
> > > 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: 2009年5月8日,周五,下午6:46
> > >
> > >
> > >
> > > xi zhao wrote:
> > > >
> > > >
> > > > Dear Sirs:
> > > > I wang to know simulate coarse-graied system using
> > gromacs, but
> > > I don not know how to use atom2cg.awk to convert CG model!
> > > > Thank you very much!
> > > >
> > >
> > > ./atom2cg_v2.1_tryout.awk my.pdb > out.pdb
> > >
> > > Note that the script available online needs to be
> modified to
> > > include a $5 between the $4 and $6 on each line, otherwise
> > you will
> > > get an incorrectly-formatted .pdb file.
> > >
> > > -Justin
> > >
> > > > 4
> > >
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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
> > > 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
> > 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
> 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
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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