[gmx-users] martini coarse-grained

[dina dusti]

----- Forwarded Message -----
From: dina dusti <dinadusti at yahoo.com>
To: XAvier Periole <x.periole at rug.nl> 
Sent: Tuesday, April 10, 2012 10:44 PM
Subject: martini coarse-grained
 

Thank you very much from your response. 

I found the coordinate file of tiofen from PRODRG and I wrote .itp file for that according to definition of molecules in martini_v2.1_aminoacids.itp file.
What is your idea about this, Please?

Best Regards
Dina



________________________________
 From: XAvier Periole <x.periole at rug.nl>
To: dina dusti <dinadusti at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Tuesday, April 10, 2012 5:16 PM
Subject: Re: [gmx-users] martini coarse-grained
 


Where did you find the topology?


On Apr 10, 2012, at 10:44 AM, dina dusti wrote:

Dear GROMACS Specialists,
>
>
>I have doubt about definition of tiofen ring in MARTINI CG force field. May I ask you to help me, Please?
>I defined if as: SC4 and SC5, that SC5 is as S-C-C and SC4 is as C-C. Is it right?
>Or should I change SC5 to C-S-C for .gro file?
>And my definition of tiofen in .itp file it is as followed , Please say me that is it right?
>
>
>
>;;;;;;  TIOFEN
>
>[moleculetype]
>; molname       nrexcl
>  TIO
         1
>
>[atoms]
>; id    type    resnr   residu  atom    cgnr    charge
>  1     SC4     1         TIO     SI1     1     0 
>  2     SC5     1         TIO     SI2    2     0 
>
>[constraints]
>; i j   funct   length
>  1 2     1     0.27
>
>
>Because I for benzene see a triangle in ngmx program, but for this see a line. Please help me to correction of mistakes.
>Thank you very much in advance.
>
>
>Best Regards
>Dina
>
>
>
>
>
>
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