Hi Priya,
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 something like:
Say for histidine
source leaprc.ff99SB
HIX = copy HIS
edit HIX
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 well.
I suggest you take a look at Tutorial A1 -
http://ambermd.org/tutorials/ for some examples. Tutorial B6 also provides a tutorial on Sirius.
Good luck,
Ross
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of priya priya
Sent: Wednesday, September 24, 2008 1:03 AM
To: amber.scripps.edu
Subject: AMBER: to prepare pdb file fro unusual amino acid.
Hi Amber Users,
I am looking for some way to prepare pdb files for a molecule with unusual amino acid, that is not incluede in Xleap of Amber.
Can anybody suggest me some tool that can be use to draw the molecule.
Regards
Priya Anand
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Received on Fri Sep 26 2008 - 05:09:34 PDT
