restraining parts of a molecule

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

Hello,
     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.
 
Thanks.
 
--Julie

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