[gmx-users] carbohydrate parameters in ffG53a6

[Jianhui Tian]

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.

Jianhui

Date: Wed, 18 Aug 2010 16:18:49 +0530 (IST)
From: parichita parichita <parichitamajumdar at yahoo.co.in
>
Subject: Re: [gmx-users] carbohydrate parameters in ffG53a6
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <456742.75700.qm at web8903.mail.in.yahoo.com>
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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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