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

[Mark Abraham]

James Starlight wrote
> 
> 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 ]
> etc
> 
> I've defined bonds of the djacent real amino acids in the specbond.dat

Seems dangerous from my memory of GFP. You should probably be making a
single residue for the whole chromophore, in which case a model that does
not need specbond.dat is possible.


James Starlight wrote
> 
> 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?
> 

If
http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database
and its links don't help, you'll have to inspect carefully your output from
pdb2gmx for clues.

Mark




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