[gmx-users] required topology stuff modification for GBSA

[Makoto Yoneya]

Dear GROMACS experts:

I'd tried to use a GBSA implicit solvent function in ver. 4.5.4.
I'd convinced the normal run with vacuo with simply high epsilon_r
setting.
After that, I'd modified the topology stuff by adding 
"[ implicit_genborn_params ]"
entry and then
implicit_solvent   = GBSA
gb_algorithm       = OBC
gb_epsilon_solvent = 78.3
in the mdp file to try a GBSA implicit solvent run.

Then I'd suffer error from grompp like as
"Fatal error:
Cannot find length for atoms 1-3 involved in angle".

Actually, there is no covalent bond between 1-3
(there is an angle with atoms 1-2-3, but these are
bonded only with 1-2 and 2-3).
I'm wondering what kinds of extra-modification in topology
stuff besides adding "[ implicit_genborn_params ]" entry
for the implicit solvent runs from the runs without it.
Any info. will be welcome.

Thank you for advance.

Makoto Yoneya, Dr.
AIST, Tsukuba
JAPAN
http://staff.aist.go.jp/makoto-yoneya/