[gmx-users] Martini

[Dariush Mohammadyani]

I think I made a mistake:

Aniline: SC4 -SC4 - SNd
Pyrrole: SC4 -SNd
Tiofen: SC4 - SC5

I am not sure...



On Thu, Mar 8, 2012 at 3:24 PM, dina dusti <dinadusti at yahoo.com> wrote:

> Dear Dariush,
>
> Thank you very much from your response.
> Then you tell me that the definition of aniline and pyrrole, is correct?
> Is your mean about SC5 for tiofen means that it is defined as SC4 and SC5
> for tiofen? indeed I had doubt about this definition because S is without H
> in tiofen.
> May I know your cause for this definition, Please?
>
> Best Regards
> Dina
>   ------------------------------
> *From:* Dariush Mohammadyani <d.mohammadyani at gmail.com>
> *To:* dina dusti <dinadusti at yahoo.com>; Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> *Sent:* Thursday, March 8, 2012 11:24 PM
> *Subject:* Re: [gmx-users] Martini
>
> SC5 does not work?
> Dariush
>
> --
> Kind Regards,
> Dariush Mohammadyani
> Department of Structural Biology
> University of Pittsburgh School of Medicine
> Biomedical Science Tower 3
> 3501 Fifth Avenue
> Pittsburgh, PA 15261
> USA
>
>
>
> On Thu, Mar 8, 2012 at 2:34 PM, dina dusti <dinadusti at yahoo.com> wrote:
>
> Dear Gromacs Specialists,
>
> May I ask you to help me for definition of pyrrole, tiofen and aniline in
> MARTINI coarse-grained force field, Please?
> I defined them as following:
> aniline (one benzene ring+NH2) = SC4, SC4, SNd
> pyrrole (one aromatic ring consists of 4 carbon and one NH) = SC4, SP1
> tiofen (one aromatic ring consists of 4 carbon and one S) = ???
> May I ask you to tell me your idea about these molecules, Please?
>
> Thank you in advance.
> Best Regards
> Dina
>
>
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-- 
Kind Regards,
Dariush Mohammadyani
Department of Structural Biology
University of Pittsburgh School of Medicine
Biomedical Science Tower 3
3501 Fifth Avenue
Pittsburgh, PA 15261
USA
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