restraining parts of a molecule

From: Stern, Julie (
Date: Sun Mar 04 2007 - 21:20:28 CST

     I'm having some problems with applying a harmonic force constant to restrain parts
of a protein. I tried a force constant of 5 and one of .5 and it has the same effect. It
blows half the molecule right out of the water shell as a result of the minimization step,
keeping a really long bond between the two parts of the molecule and an empty space
where that part of the molecule was.
Here is the code excerpt:
# restraints
constraints on
consexp 2
consref res.pdb
conskfile restrained_res.pdb
conskcol O

Does anyone have any suggestions of what the force constant should be or what
else I can check? Any ideas on why this might be happening? I doubled checked that the
res.pdb and restrained_res.pdb have the same coordinates to start with so nothing is
offset to begin with.

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:46:04 CST