----- Forwarded Message -----
From: dina dusti <dinadu...@yahoo.com>
To: XAvier Periole <x.peri...@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.peri...@rug.nl>
To: dina dusti <dinadu...@yahoo.com>; Discussion list for GROMACS users
<gmx-users@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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