[gmx-users] martini coarse-grained

dina dusti dinadusti at yahoo.com
Tue Apr 10 20:29:51 CEST 2012

----- 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

 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
>; molname       nrexcl
>  TIO
>; id    type    resnr   residu  atom    cgnr    charge
>  1     SC4     1         TIO     SI1     1     0 
>  2     SC5     1         TIO     SI2    2     0 
>; 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
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