Dear Priya,
Have a look at the LEAP manual:
# create peptide with sequence PCEW
peptide = sequence { NPRO CYS GLU CTRP }
# set dihedral angles of residues 2 and 3
impose peptide { 2 3 } {
# psi
{ N CA C N 145.0 }
# phi
{ C N CA C -75.0 }
# omega (trans)
{ CA C N CA 180.0 }
}
You have to be careful about which dihedral you change: The residue number
is applied to the first atom of the definition, e. g.
impose x { 4 } { { C N CA C 0.0 } }
imposes an angle of 0° to the C-N-CA-C dihedral around the N-CA bond of
residue 5!
Good luck,
´
Hannes
_____
Von: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] Im Auftrag von
priya priya
Gesendet: Mittwoch, 13. September 2006 11:03
An: amber.scripps.edu
Betreff: AMBER: how to feed dihedral angles of our choice to the linear
sequence in amber8
Dear
I have loaded a linear sequence of 15 residue peptide....now i want to
change the dihedral angles and want to start with the different
conformation.
Please suggest me the path for that.
With Regards
Priya
_____
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Sep 17 2006 - 06:07:05 PDT
