[AMBER] non standard Alanine

From: Massimiliano Porrini <M.Porrini.ed.ac.uk>
Date: Fri, 4 Mar 2011 14:41:59 +0000

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

- 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,

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
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Received on Fri Mar 04 2011 - 07:00:04 PST
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