[gmx-users] carbohydrate parameters in ffG53a6

[Justin A. Lemkul]

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.
> 
> --- On Wed, 18/8/10, Jianhui Tian <jianhuitian at gmail.com 
> <mailto:jianhuitian at gmail.com>> wrote:
> 
> 
> From: Jianhui Tian <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>
> 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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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