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

[Mark Abraham]

anoop dimri wrote:
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> 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.

See http://wiki.gromacs.org/index.php/specbond.dat

Mark