[gmx-users] Adding New Residue to the Gromos 53.6 ff

James Starlight jmsstarlight at gmail.com
Sun Aug 5 15:12:16 CEST 2012

Dear Gromac's users!

I'm working with the GFP protein which has chromophore (CRO) group
which is covalently bonded to the protein. I want to add new residue
to the Gromos 53.6 ff. by means of algorithm described here.

For that I've coppied files to my local work dirr and modify all of
them in accordance to the above tutorial- I've coppied .itp of CRO to
the aminoacids.rtp

[ CRO ]
[ atoms ]

I've defined bonds of the djacent real amino acids in the specbond.dat

Finally I've defined CRO (as the protein) in the residuetypes.dat

When I've try use pdb2gmx I've obtain error

Fatal error:
Residue 'CRO' not found in residue topology database

What I've done wrong?


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