Adding a new bond to CHARMM

From: DimitryASuplatov (
Date: Sat Apr 25 2009 - 08:23:19 CDT


I have a covalent bond between Tyr and Cys in my structure. I want to
preserve this bond for molecular dynamics.
I was recently using GROMACS. So to introduce this bond I had to

1/ Specify the atom-atom distance for this bond in specbond.dat file.
In case of such distance occurs Cys2 and Tyr2 topologies are used
instead of Cys and Tyr default ones.
2/ Specify new protonation state for Tyr2 residue in ff protonation file
3/ Write a new topology to ff topology file file

Could you briefly associated those stages to NAMD?
I appreciate your time.

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