[gmx-users] required topology stuff modification for GBSA

[Makoto Yoneya]

Dear GROMACS users:

This is self-reply to resolve the following error I'd met.

> Then I believe the error
> > "Fatal error:
> > Cannot find length for atoms 1-3 involved in angle".
> occurs with some side-effects from the implicit solvent setting.

I'd found that the topology stuff should be more strictly
written with implicit_solvent=GBSA than that with
implicit_solvent=no.
For simple example, all-atom CH4 molecule has five atoms
and four bonds and six angles.
If I only have five angles by mistake, it is tolerant
with implicit_solvent=no but result in the error above with
implicit_solvent=GBSA.
It means you should check the number of angles,
if you've got the error when you change implicit_solvent=no
to implicit_solvent=GBSA.

Hope it helps.

Regards,

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