[gmx-users] trouble adding c-terminal formyl group to ff*.rtp
feenstra at chem.vu.nl
Fri Oct 10 09:15:02 CEST 2003
Senthil Kandasamy wrote:
> I need to define a dihedral that involves the N atom of the "next"
> aminoacid. How do I incorporate this into the hdb file? (As I
> understand, the "previous carbon " can be designated as a -C.)
Quite simple, '+C'. But you should also check which dihedrals are
already included in the normal aa rtp entries (this differs per ff),
some include a dihedral to the previous residue, and others to the next.
In short, do it for the termini as it is done for the residues, which
means that you need '+C' only on the C-term, or '-C' only on the N-term.
Finally, for running things through pdb2gmx, the new terminal residues
must also be in 'aminoacids.dat' for pdb2gmx to recognize them as part
of the protein.
> (Thought: Am I better off defining the C-terminal formyl group in the
> tdb file?)
Maybe. It doesn't look much more difficult than a -COO group. The file
syntax is somewhat less easy to work with than the .rtp.
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