[gmx-users] carbohydrate parameters in ffG53a6

[Justin A. Lemkul]

Jianhui Tian wrote:
> Hi Justin,
> 
> I compare the few sugars (Glc, Gal, Man), their parameters are indeed 
> nearly identical except for some improper dihedrals.
> Then I can transfer these parameters to other sugars.

Sounds about right.

> How about Glycolipid? For example, the link "phosphatidyl-myo-inositol". 
> Do you have any suggestion?

Yes, consult the literature.  There are several recent simulation studies (and
some that are not so recent) about glycolipids.  I would review the methodology
used in that type of work.

-Justin

> Thanks.
> 
> Jianhui
> 
> Date: Wed, 18 Aug 2010 12:45:15 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> Subject: Re: [gmx-users] carbohydrate parameters in ffG53a6
> To: Discussion list for GROMACS users <gmx-users at gromacs.org 
> <mailto:gmx-users at gromacs.org>>
> Message-ID: <4C6C0E1B.1020107 at vt.edu <mailto:4C6C0E1B.1020107 at vt.edu>>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> 
> 
> Jianhui Tian wrote:
>  > Hi Parichita,
>  >
>  > Thanks for the suggestion. However, the question is what parameters from
>  > ffG53a6 can be used for not included sugars or glycolipid. I guess you
>  > can not simply use the charge, angle and dihedral values based on the
>  > atom types from 53a6.
>  >
> 
> Gromos building blocks are quite transferable between different molecules.
> Compare a few sugars - the parameters are nearly identical.  That is one 
> of the
> central features of this particular force field, that functional group 
> charges
> should be as versatile as possible.
> 
> As for the lipids, there are new versions of 53A6 (which I believe have been
> uploaded to the Gromacs site) that perform substantially better than the
> built-in parameters.  The long acyl chains are not particularly accurate 
> in the
> default 53A6.
> 
> -Justin
> 
>  > Jianhui
>  >
>  > Date: Wed, 18 Aug 2010 16:18:49 +0530 (IST)
>  > From: parichita parichita <parichitamajumdar at yahoo.co.in 
> <mailto:parichitamajumdar at yahoo.co.in>
>  > <mailto:parichitamajumdar at yahoo.co.in 
> <mailto:parichitamajumdar at yahoo.co.in>>
>  >  >
>  > Subject: Re: [gmx-users] carbohydrate parameters in ffG53a6
>  > To: Discussion list for GROMACS users <gmx-users at gromacs.org 
> <mailto:gmx-users at gromacs.org>
>  > <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>  >
>  > Message-ID: <456742.75700.qm at web8903.mail.in.yahoo.com 
> <mailto:456742.75700.qm at web8903.mail.in.yahoo.com>
>  > <mailto:456742.75700.qm at web8903.mail.in.yahoo.com 
> <mailto:456742.75700.qm at web8903.mail.in.yahoo.com>>>
>  > Content-Type: text/plain; charset="iso-8859-1"
>  >
>  > Hi Jianhui,
>  >  For your sugar part you can use PRODRG, which will convert coordinates
>  > for small molecules in PDB format (or simple text structures) to the
>  > following topology formats: GROMOS, GROMACS and  from literature if you
>  > can find out the parameters of ffG53a6 force field,  then you can
>  > correct the charge, angle and dihedral values that you are collected
>  > from the PRODRG. Hope this will help you.
>  > Regards...
>  > Parichita...........
>  >
>  >
>  >
>  >
>  > Parichita Mazumder
>  > Research Fellow
>  > C/O Dr. Chaitali Mukhopadhayay
>  > Department of Chemistry
>  > University of Calcutta
>  > 92,A P C Road
>  > Kolkata-700009
>  > India.
>  >
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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