Dear Amber User,
I am trying to restrain torsions and bond angles to do
minimizations using sander_classic (do not want Cartesian coordinate
restraints). I have tried to use the restrainTorsion command in xleap,
which for all I can tell is working fine (desc [unit] tells me that the
restraints I specified has been applied.) But, after I run sander and
look at my coordinates I don't see the effect of the restraints. However,
I also tested the restrainBond and restrainAngle commands and found that
they do indeed restrain the defined internals during minimization. Do
anyone know what could be wrong with the Torsional restraints? Is there a
flag to turn on these restraints?
As an alternative, I am trying to use NMR-refinement restraints
to define the torsions in sander. I ran into a problem with makeANG_RST
looking for tordef.lib and the help file through the incorrect path:
/thr/cauchy/amber42/src/nmr_aux/prepare_input/makeANG_RST.help
The files exist but the path is hard coded into the program. The problem
can be avoided by explicitly listing the correct path for tordef.lib, but
the coding should be fixed. Although the torsional restaint was applied I
have been unable to figure out how to apply different restraint to
different internals. And suggestions?
Thanks for your help!
Manoj Cheriyan
University of Michigan
Ann Arbor, MI
Received on Wed Jul 11 2001 - 15:19:31 PDT
