[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
>     <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
>     <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>
>      > 
>        <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>
>      > 
>        <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
>      >      >       
>     <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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>      >      >     -- ========================================
>      >      >
>      >      >     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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