AMBER Archive (2006)

Subject: AW: AMBER: how to feed dihedral angles of our choice to the linear sequence in amber8

From: Hannes Barsch (hbarsch_at_physik.uni-bielefeld.de)
Date: Wed Sep 13 2006 - 08:54:54 CDT

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_at_scripps.edu [mailto:owner-amber_at_scripps.edu] Im Auftrag von
priya priya
Gesendet: Mittwoch, 13. September 2006 11:03
An: amber_at_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

  _____

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