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 <[email protected] > Subject: Re: [gmx-users] carbohydrate parameters in ffG53a6 To: Discussion list for GROMACS users <[email protected]> Message-ID: <[email protected]> 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 <[email protected]> wrote: From: Jianhui Tian <[email protected]> Subject: [gmx-users] carbohydrate parameters in ffG53a6 To: [email protected] 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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