[gmx-users] how to show structure results in Martini coarse-grained simulation?

[Justin A. Lemkul]

xi zhao wrote:
> 
> 
> Yes, the PSF file has NBOND section and the script finished without 
> any errors! But it does not show any bonded!
> Thank you！

Can you send me your coordinate file and .psf file (off-list) so I can see if 
there's anything to diagnose?  If you have an NBOND section, the script has done 
its job and should work.

-Justin

> 4 
> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
> 
> --- *10年5月7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 show structure results in Martini
>     coarse-grained simulation?
>     收件人: "Gromacs Users' List" <gmx-users at gromacs.org>
>     日期: 2010年5月7日,周五,下午7:10
> 
> 
> 
>     xi zhao wrote:
>      >
>      > Yes， I load my coarse-grained PDB ,then load ps as data, but the
>     stucture still was full of points .
>      >
> 
>     Is a proper "!NBOND" section generated in your .psf file?  If the
>     script finishes without any errors, the output should be viable.
> 
>     -Justin
> 
>     -- ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     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
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================