[gmx-users] how to use atom2cg.awk
xi zhao
zhaoxiitc2002 at yahoo.com.cn
Mon May 11 14:16:46 CEST 2009
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 !
--- 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>
>
> --- *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,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>>
> >
> > --- *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>>/* 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: "Discussion list for GROMACS users"
> <gmx-users at 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
> > <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>>>
> > >
> > >
> > >
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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
>
> ========================================
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
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> Please search the archive at http://www.gromacs.org/search before
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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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