AMBER Archive (2008)
Subject: Re: AMBER: to prepare pdb file fro unusual amino acid.
From: priya priya (priyaanand_27_at_yahoo.co.in)
Thanks for your suggestion, the unusual amino acid(peptoid) is just a simple modification of amino acids, i have to delete a bond a create a bond and then save the pdb file for that. I will try both xleap and sirius program for that.
----- Original Message ----
From: Ross Walker <ross_at_rosswalker.co.uk>
Sent: Thursday, 25 September, 2008 8:25:21 PM
Subject: RE: AMBER: to prepare pdb file fro unusual amino acid.
How unusual is it? If it is a simple modification of an existing
amino acid then this should be fairly easy to do in xleap. You just do
Say for histidine
HIX = copy HIS
Then you can draw in / delete atoms, set the atom types etc. You
will of course need to calculate the charges for this amino acid, add any
missing parameters before you can simulate it in AMBER. If the amino acid is
more complicated then you probably want to use a program more suited to 3D
drawing - http://sirius.sdsc.edu works
I suggest you take a look at Tutorial A1 - http://ambermd.org/tutorials/ for some
examples. Tutorial B6 also provides a tutorial on Sirius.
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