[gmx-users] GBSA problem

susanta haldar susantahaldar at gmail.com
Wed May 29 15:01:31 CEST 2013

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.

More information about the gromacs.org_gmx-users mailing list