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

[xi zhao]

Dear Sir :
The script require what format for top file? my top file is here: 

;
; Example topology file for MARTINI 2.0
;
; First include the file containing all particle definitions,
; the interaction matrix, plus the topology for water.
#include "martini_v2.1.itp"
#include "martini_v2.0_ions.itp"
#include "martini_v2.0_lipids.itp"
#include "3ehz.itp"
; Include Position restraint file
#ifdef POSRES
#include "s.itp"
#endif
[ system ]
CGprotein  ion channel
[ molecules ]
; name  number
Protein     1
POPC       502
W         18934
but run top2psf.pl 
"Cannot open atoms for reading: No such file or directory"
please help me!


--- 10年5月3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 show structure results in Martini coarse-grained simulation?
收件人: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
日期: 2010年5月3日,周一,上午8:08




xi zhao wrote:
> Dear user:
> how to show struture or conformation in Martini coarse-grained simulation, using VMD or other?
> Please give me some suggestion!
> thank you!

What kind of rendering do you want to do?  There are some scripts linked below to render bonds in a CG structure.

http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD#VMD_and_coarse-grained_simulations

-Justin

> 
> 
> 4 <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
> 
> 
>  

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

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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