[gmx-users] carbohydrate parameters in ffG53a6

[Jianhui Tian]

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

Jianhui

Date: Wed, 18 Aug 2010 12:45:15 -0400
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] carbohydrate parameters in ffG53a6
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <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>
>  >
> 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: <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.
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100818/42f6b0cd/attachment.html>