AMBER Archive (2009)

Subject: [AMBER] Question about the debug forces

From: Faezeh Salehi (salehi.faezeh_at_gmail.com)
Date: Wed Sep 02 2009 - 16:30:47 CDT

I'm running Amber 10 and I've used the do_debugf=1, dumpfrc=1,
to make sander create the forcedump.dat.

I'm using the following input file:
cat << EOF > min.in
minimization
&cntrl
imin = 1, maxcyc = 0,
irest = 0, ntx = 1,
ntb = 0, ntp = 0,
ntpr = 100,
nsnb = 10,
cut = 10.0,
lastist = 10000000,
igb = 1,
&end
&debugf
  do_debugf=1, dumpfrc=1,
&end
EOF

I'm using mutate.pl to change a residue. I expected that the forces
on the atoms in this residue would change before and after
minimization.

I tried changing maxcyc=0 to maxcyc=1000, but they were still the
same. I also tried minimizing the protein and then running the debug
script to dump the forces. In all three cases, I got the same
results.

Does anyone know what's going on?
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