[gmx-users] trouble adding c-terminal formyl group to ff*.rtp

[Anton Feenstra]

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.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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