Dear all,
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?
- How can I change the improper torsion parameters for the D-Ala
residue in order to keep it as D-isomer?
If the answer to both questions is "antechamber" I would throw another
question and a following
consideration:
- Does antechamber re-calculate the parameters even for the standard
amino acids present in my peptide?
I have already run antechamber and as far as I read on the manual in
my case I should use the
option `-at amber`, since my peptide has only the D-Ala as
non-standard amino acid.
But when I edit the .prm file produced I see only one type of residue:
i.e. Ala (which was the first
in the sequence).
And if I run `ambpdb`, the sequence of the output pdb has only the
name `ALA` for all the residues.
Does this mean that standard amino acids of my peptide are
re-parametrized through antechamber?
Any hint and suggestion would be really appreciated.
Thank you in advance,
MP
--
Dr Massimiliano Porrini
P. E. Barran Research Group
Institute for Condensed Matter and Complex Systems
School of Physics & Astronomy
The University of Edinburgh
James Clerk Maxwell Building
The King's Buildings
Mayfield Road
Edinburgh EH9 3JZ
Tel +44-(0)131-650-5229
E-mails : M.Porrini.ed.ac.uk
mozz76.gmail.com
maxp.iesl.forth.gr
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Received on Fri Mar 04 2011 - 07:00:04 PST
