AMBER Archive (2003)

Subject: AMBER: The FCAP parameter in amber7

From: Thomas Steinbrecher (thomas.steinbrecher_at_physchem.uni-freiburg.de)
Date: Fri Aug 22 2003 - 04:21:35 CDT

Dear AMBER users,

I have a question concerning the FCAP parameter in a
calculation of a protein ligand complex including a cap of
water molecules.
I am conducting my simulation along the lines of the
biotin/streptavidin tutorial from the AMBER homepage, that
means I prepared parameters and coordinates for my complex
with leap, added a cap of water molecules and defined a
belly of moveable residues that includes the water cap
along with a cutout of the protein around my ligand.

When I started my first equilibration runs I encountered
the
"systen has extended beyond the extent of the virtual
box"-problem described in the mailing list archives.

As suggested there I added FCAP=1 to my input file for
sander. I thought that would place a small (1
kcal/(mol*A*A)) restraint on my cap waters fixing them
close to their starting places.
Indeed the simulation runs fine for some 100ps now, but
when I look at the rmsd, it is quite stable at ~1.3 A for
my ligand and protein as expected (or hoped at least) but
for the water molecules the rmsd is rising constantly. Also
the restraint energy is 0 in my output files. I wonder how
these two things can be if my waters are restrained.

Can someone explain to me how the fcap parameter works?

Many thanks in advance,

Thomas Steinbrecher

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