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" <[email protected] <mailto:[email protected]>>
Subject: Re: [gmx-users] carbohydrate parameters in ffG53a6
To: Discussion list for GROMACS users <[email protected]
<mailto:[email protected]>>
Message-ID: <[email protected] <mailto:[email protected]>>
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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 <[email protected]
<mailto:[email protected]>
> <mailto:[email protected]
<mailto:[email protected]>>
> >
> Subject: Re: [gmx-users] carbohydrate parameters in ffG53a6
> To: Discussion list for GROMACS users <[email protected]
<mailto:[email protected]>
> <mailto:[email protected] <mailto:[email protected]>>
>
> Message-ID: <[email protected]
<mailto:[email protected]>
> <mailto:[email protected]
<mailto:[email protected]>>>
> 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
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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