I'm trying to setup a simulation of 2 molecules of beta-D-glucose in vacuum at 100k. I'm using the OPLS/AA force field, have a pdb file that looks good in VMD, and have started creating the .itp file. I've described the bonds, pairs, and angles but am having difficulty completing the parameterization:
1. If I run grompp, I get the "no default angle types" error for the angle C1-O-H, where C1 refers to carbon-1, bonded to the O in the ring. If I comment out just that angle in the .itp file, grompp runs without problems. I assume this means the OPLS force field doesn't have an angle type corresponding to that part of the molecule. Why is this and what should I do about it? 2. I don't know how to specify dihedrals and improper dihedrals for glucose. What's the best place to learn this? Thanks, Daniel -- View this message in context: http://gromacs.5086.n6.nabble.com/How-to-parameterize-glucose-tp5006390.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
