[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
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
>
>
>
>
>
>
>--
>gmx-users mailing list gmx-users at gromacs.org
>http://lists.gromacs.org/mailman/listinfo/gmx-users
>Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>Please don't post (un)subscribe requests to the list. Use the
>www interface or send it to gmx-users-request at gromacs.org.
>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120410/ceefa90c/attachment.html>
More information about the gromacs.org_gmx-users
mailing list