Hi Parichita,<br><br>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.<br>
<br>Jianhui<br><br>Date: Wed, 18 Aug 2010 16:18:49 +0530 (IST)<br>
From: parichita parichita <<a href="mailto:parichitamajumdar@yahoo.co.in">parichitamajumdar@yahoo.co.in</a><div id=":7k">><br>
Subject: Re: [gmx-users] carbohydrate parameters in ffG53a6<br>
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Hi Jianhui,<br>
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.<br>
Regards...<br>
Parichita...........<br>
<br>
<br>
<br>
<br>
Parichita Mazumder <br>
Research Fellow<br>
C/O Dr. Chaitali Mukhopadhayay<br>
Department of Chemistry<br>
University of Calcutta<br>
92,A P C Road<br>
Kolkata-700009<br>
India.<br>
<br>
--- On Wed, 18/8/10, Jianhui Tian <<a href="mailto:jianhuitian@gmail.com">jianhuitian@gmail.com</a>> wrote:<br>
<br>
<br>
From: Jianhui Tian <<a href="mailto:jianhuitian@gmail.com">jianhuitian@gmail.com</a>><br>
Subject: [gmx-users] carbohydrate parameters in ffG53a6<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Date: Wednesday, 18 August, 2010, 10:16 AM<br>
<br>
<br>
Hi,<br>
<br>
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?<br>
<br>
Jianhui<br>
</div>