[gmx-users] Which force field to use to study intra-molecular hydrogen bonding?

Peggy Yao peggy.yao at gmail.com
Wed Feb 18 00:36:24 CET 2009

Dear all,

I'd like to study intra-molecular hydrogen bonding. Which force field would
you recommend?

I have been working on G43a1 and OPLS. OPLS seems quite good. It places all
H-atoms. However, G43a1 only considers H-atoms on N-atoms, but not C-atoms.
Even if I input a fully-added-H-atom PDB file to pdb2gmx:

pdb2gmx -ff G43a1 -f 1eia_hadded.pdb -p 1eia.top -o 1eia.pdb -water spce

1eia.pdb still only constains H-atoms on N-atoms. I believe, by default,
"-ignh" has value "no", which means if I don't put "-ignh", it should read
in all the H-atoms in the input PDB file.

Besides OPLS, is there any other good force field to study hydrogen bonding?

Is there any way to make G43a1 to take all H-atoms into account?

Thanks a lot!

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