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 -----Inline Attachment Follows----- -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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