[gmx-users] bond, angles and dihedrals in the topology file

[faride badalkhani]

Dear all,

Could you tell me what is wrong when there are some strange bond, angles
and dihedrals in the topology file after executing pdb2gmx command?
for example atoms 1 and 27 do not have any connectivity, but pdb2gmx
generate them as [bonds]. A similar problem occurs in case of angles and
dihedrals.

Truly yours,
Farideh