[gmx-users] how to use atom2cg.awk

[xi zhao]

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! 
Thank you very much! 
Best regards!   




--- 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>
> 
> --- *09年5月8日，周五, 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: "Discussion list for GROMACS users" <gmx-users at 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>>
>      >
>      >
>      >
>     ------------------------------------------------------------------------
>      > 好玩贺卡等你发，邮箱贺卡全新上线！
>     <http://cn.rd.yahoo.com/mail_cn/tagline/card/*http://card.mail.cn.yahoo.com/>
> 
>      >
>      >
>      >
>     ------------------------------------------------------------------------
>      >
>      > _______________________________________________
>      > gmx-users mailing list    gmx-users at gromacs.org
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>
>      > http://www.gromacs.org/mailman/listinfo/gmx-users
>      > Please search the archive at http://www.gromacs.org/search before
>     posting!
>      > Please don't post (un)subscribe requests to the list. Use the www
>     interface or send it to gmx-users-request at gromacs.org
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org>.
>      > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
>     -- ========================================
> 
>     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
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>
>     http://www.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at http://www.gromacs.org/search before
>     posting!
>     Please don't post (un)subscribe requests to the list. Use the
>     www interface or send it to gmx-users-request at gromacs.org
>     <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org>.
>     Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
> ------------------------------------------------------------------------
> 好玩贺卡等你发，邮箱贺卡全新上线！ <http://cn.rd.yahoo.com/mail_cn/tagline/card/*http://card.mail.cn.yahoo.com/> 

-- ========================================

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
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php



      ___________________________________________________________ 
  好玩贺卡等你发，邮箱贺卡全新上线！ 
http://card.mail.cn.yahoo.com/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090511/2fd30557/attachment.html>