Dear Massimiliano,
> I would need to model a 8 residues long peptide, whose first (N-term) residue
> is the D-isomer of the Alanine and whose C-terminus is capped with -NH2 group.
>
> I would like ask you the following questions:
>
> - Is there any residue name recognized by tleap that I could use for
> the capping group -NH2?
there exists the c-terminal capping group NHE (available with standard
parm99SB), which is exactly what you want.
> - How can I change the improper torsion parameters for the D-Ala
> residue in order to keep it as D-isomer?
As far as I know, you do not need any special parameters for D-amino
acids. When I remember correctly, Carlos Simmerling once wrote here on
the list, that they tested the parameters for both, L and D configurations.
So, if your initial structure is the D-isomer an you do not simulate at
high temperatures (like REMD), then you do not need any additional
parameters or restraints here (specialists, please correct me, if I'm
wrong!).
Regards,
Anselm
Bioinformatik
Institut für Biochemie
Friedrich-Alexander-Universität Erlangen-Nürnberg
Germany
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Received on Fri Mar 04 2011 - 08:00:03 PST
