[gmx-users] carbohydrate parameters in ffG53a6

[Justin A. Lemkul]

Rasoul wrote:
> For the sugar parameters you can use Glycam parameters  
> http://glycam.ccrc.uga.edu/documents/gl_params.jsp
> After with specific script it can be convert to Gromac readable file:
> http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Other_software
> 

Mixing and matching force field parameters is a very bad idea.  To have a valid
physical model, parameters should be derived in compatible ways.

-Justin

> I hope it would be useful for you.
> 
> Rasoul
> On Wed, Aug 18, 2010 at 6:45 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     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.
> 
>         --- On Wed, 18/8/10, Jianhui Tian <jianhuitian at gmail.com
>         <mailto:jianhuitian at gmail.com> <mailto:jianhuitian at gmail.com
>         <mailto:jianhuitian at gmail.com>>> wrote:
> 
> 
>         From: Jianhui Tian <jianhuitian at gmail.com
>         <mailto:jianhuitian at gmail.com> <mailto:jianhuitian at gmail.com
>         <mailto:jianhuitian at gmail.com>>>
> 
>         Subject: [gmx-users] carbohydrate parameters in ffG53a6
>         To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>         <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> 
>         Date: Wednesday, 18 August, 2010, 10:16 AM
> 
> 
>         Hi,
> 
>         I want to do some simulations about carbohydrates and
>         glycolipid. In the ffG53a6.rtp file, I just see limited
>         parameters for carbohydrate, like monosaccharide Glucose,
>         Mannose and Galactose. What parameters can be used for others
>         like arabinose? Also, is there any parameters available in the
>         Gromacs force field for glycolipid?
> 
>         Jianhui
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
> 
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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

========================================