[gmx-users] martini coarse-grained
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?
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?
>; molname nrexcl
>; 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.
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