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
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--- *09年5月11日，周一, Justin A. Lemkul /<jalem...@vt.edu>/* 写道：
发件人: Justin A. Lemkul <jalem...@vt.edu>
主题: Re: [gmx-users] how to use atom2cg.awk
收件人: "Gromacs Users' List" <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
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>
> --- *09年5月8日，周五, 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 use atom2cg.awk
> 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>>
> 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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> jalemkul[at]vt.edu | (540) 231-9080
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-- ========================================
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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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Department of Biochemistry
Virginia Tech
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http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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