[gmx-users] How to parameterize glucose

[dreda]

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.