[gmx-users] pdb2gmx: Bond type, Angle type, Dihedral angle type missing in topology file.

anoop dimri anoop.dimri at gmail.com
Mon Feb 2 07:07:55 CET 2009

Hi all gromacs users.

I am using gromacs v 3.3.3 on 32 bit system with suse-linux. I am working
with protein and using Gromos96 43a1 force-field. When i generate topology
file through pdb2gmx, i found that some bond types, angle types and Dihedral
angle types are missing. Some of these are related to S-S bridge and
remaining are related to HEME's Fe (intra-residual and inter-residual).
Should I fill this manually in top file ? If   anyone know why this thing is
happening, so please give me  suggestion.

Thank you.

Anoop Dimri
NIPER Kolkata
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