On 06/24/2011 02:21 PM, Makoto Yoneya wrote:
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).
You don't say what your force field is, but those symptoms are
suggestive of a problem with CHARMM force field lacking Urey-Bradley
interaction parameters for atoms 1-2-3. If so, this is not a GB problem
per se.
Mark
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/
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