AMBER Archive (2006)

Subject: AMBER: problem with amber 9 and igb=5

From: M. Scott Shell (shell_at_maxwell.compbio.ucsf.edu)
Date: Wed Jun 07 2006 - 20:06:02 CDT

Hello,

I am having a problem using amber 9 with igb=5 to minimize a short
peptide sequence in sander. For some reason, sander often hangs during
the minimization procedure, although sometimes it seems to work just
fine. Using the same input files amber 8 always works smoothly without
hanging, however. Amber 9 also seems to work smoothly with igb=7 and
igb=1. I am wondering if this is a bug in amber 9 or simply a hiccup in
my input files or something specific to my system. The inputs are below
(the restraints.txt file mentioned is empty for this particular run).
Any thoughts?

Many thanks,

M. Scott Shell
Postdoctoral scholar, Dill group
Department of Pharmaceutical Chemistry
University of California San Francisco

---TLEAP INPUT (seems to work fine)---
source leaprc.ff96
set default PBradii mbondi2
seq = {ACE ASP LEU GLY VAL LYS GLU LYS LEU ILE GLU LYS ALA NME}
sys = loadPdbUsingSeq init04.pdb seq
check sys
saveAmberParm sys prmtop.parm7 tleapout.crd
savepdb sys tleapout.pdb
quit

---SANDER INPUT---
Minimization - steepest descent followed by conj grad
 &cntrl
  imin=1, maxcyc=1050, ncyc=1000,
  igb = 5, gbsa = 1,
  cut = 16.0,
  ntc = 1, ntf = 1, tol = 1.0d-8,
  ntb = 0, iwrap = 0,
  ntpr=100, ntwr=1000,
  nmropt = 1,
  ntr = 0,
 &end
 &wt type='REST', istep1=0, istep2=100, value1=1.0,
     value2=1.0, &end
 &wt type='END' &end
 DISANG=restraints.txt

END
END

---COMMAND LINE---
sander -O -i minin.txt -o minout.txt -p prmtop.parm7 -c tleapout.crd -r
minout.crd -e minene.txt -inf mininfo.txt

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