[gmx-users] GBSA problem

[susanta haldar]

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.