Dear gmxusers,
I am using gromacs version 4.5.4 and i am simulating a
surface upon base pairs on it. I would like perform simulation with the
GBSA implicit solvent model and I have tried that but one problem occurs
during running. Actually grompp has having some problem with the recent
topology of the surface. The error is given below--
Fatal error: Cannot find length for atoms 1-3 involved in angle".
the input file is like that--
implicit_solvent = GBSA
gb_algorithm = OBC
rgbradii = 0.00
gb_epsilon_solvent = 80
sa_surface_tension = 0.0054
I have checked the topology where 1 and 2 has a covalent bond and 2 and 3
does the same and there is a angle in between.
I am surprised what kind of extra-modification would require to restrict
the error shown by grommp.
I will be very much happy if somebody comes forward and helps me to get rid
of the problem.
thanking you in advance,
--
Susanta Haldar
Institute of Organic Chemistry and Biochemistry
Academy of Sciences of the Czech Republic.
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