[MMTK] Change of amino acid definition file

Berit Hinnemann Berit.Hinnemann@fysik.dtu.dk
Tue, 16 Oct 2001 11:52:41 +0200

Hi Konrad,

I would like to change an amino acid definition file while MMTK is
running. I defined a new amino acid with
"defineAminoAcidResidue('glycinexx', code3='gxx', code1='x')", then I
read in a PDB file, and then I ask for the energy or do a minimization.

If I then change the file "glycinexx" (I am changing the partial
charges) and then ask for the energy, the changes are not taken into
account, so the file is apparently not reread. I have tried to create
the universe and the protein new, but that doesn't help. So the partial
charges are not reread out of the definition file each time I ask for an
energy, but cached somewhere?

I am also making changes in the AMBER parameter modification file, while
MMTK is running, and this file is read whenever I create the universe
new. When is the amino definition file actually read and how could I
enforce it to be reread?

Thanks a lot,

Berit Hinnemann
Center for Atomic-Scale Materials Physics (CAMP)
Dept. of Physics, Technical University of Denmark
Building 307, DK-2800 Lyngby, Denmark 
Phone: +45 4525 3209, Fax: +45 4593 2399