[gmx-users] carbohydrate parameters in ffG53a6

[parichita parichita]

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> wrote:


From: Jianhui Tian <jianhuitian at gmail.com>
Subject: [gmx-users] carbohydrate parameters in ffG53a6
To: 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 

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