[gmx-users] carbohydrate parameters in ffG53a6
Justin A. Lemkul
jalemkul at vt.edu
Thu Aug 19 13:03:19 CEST 2010
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.
> 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
> 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.
> > 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.
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users