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 M.S.(Pharmacoinformatics) NIPER Kolkata INDIA
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