[gmx-users] CHARMM36 and carbohydrates

Timothy Click tclick at nctu.edu.tw
Wed Jun 18 06:29:06 CEST 2014

Greetings from Taiwan. I am having a bit of trouble setting up a carbohydrate in Gromacs. I have a PDB file that has a glucan chain between a graphene bilayer, but when I run pdb2gmx, it complains of missing atoms. Yes, an oxygen is supposed to be missing because of the 1,4 beta glycosyl linkage. I want to use the CHARMM36 force field, which has the individual carbohydrate defined. If I use CHARMM, I have no problem setting this up (initially setup to use NAMD), but I prefer Gromacs.

Any help is appreciated.

柯明 Timothy H. Click, Ph.D.
Department of Biological Science and Technology
Institute of Bioinformatics and Systems Biology
National Chiao Tung University
208 Lab Building 1, 75 Bo-Ai St.
Dong District, Hsinchu, Taiwan 30062
tclick at nctu.edu.tw

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