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

faride badalkhani farideh.khamseh at gmail.com
Wed Sep 30 13:21:42 CEST 2015


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


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