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
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Received on Fri Sep 26 2008 - 05:10:53 PDT
