[AMBER] xleap does not want to impose my dihedrals

From: <steinbrt.rci.rutgers.edu>
Date: Tue, 15 Feb 2011 13:27:27 -0500 (EST)


I came across a strange error when trying to use xleap to build an
alpha-helical peptide. Reduced to the minimum it looks like this:

> source leaprc.ff10
> foo = sequence { ALA ALA ALA }
> impose foo { 2 } { { N CA C N -40.0 } }
impose: Illegal angle internal definition
> impose foo { 2 } { { N CA 2.0 } }

Imposing the distance change works, but xleap seems not to recognise my
dihedral definition. From the error, it seems not to recognise that this
is supposed to be a dihedral. Im puzzled what went wrong here, as the
example is pretty much copied from the manual. Also, the problem lies not
in using the name N twice, or using atoms from different residues since:

> impose foo { 2 } { { N CA C O -40.0 } }
impose: Illegal angle internal definition

fails in the same way (as does using tleap).

before I did deeper, has anyone seen this kind of error?

Kind Regards,


Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Tue Feb 15 2011 - 10:30:06 PST
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