AMBER Archive (2005)

Subject: RE: AMBER: Protein with structural ions

From: Kara Di Giorgio (kdigiorgio_at_sbcglobal.net)
Date: Tue Apr 12 2005 - 10:51:32 CDT

I'm not sure if I formatted everything correctly. It ran, but the
calcium that I'm trying to restrain is still leaving the protein after
8 ps like the restraints weren't there at all. Could someone look at
my md.in and restraints.f files to see if they can see anything majorly
incorrect? I'll include them in this message.

Thanks,

Kara Di Giorgio

md.in

stromelysin and ph1ala MD G4eneralised Born, 12 angstrom cut off Ca
restraints
  &cntrl
   imin = 0, ntb = 0,
   igb = 1, ntpr = 100, ntwx = 100,
   ntt = 3, gamma_ln = 1.0,
   tempi = 300.0, temp0 = 300.0
   nstlim = 10000, dt = 0.001,
   nmropt = 1,
   cut = 12
  /
  &wt type="REST", istep1=0, istep2=10000, value1=1.0, value2=1.0,
  /
  &wt type='end'
  /
DISANG = enzph1alarestraints.f

restraints.f

# distance restraints prepared by hand for Ca
#( oxygen 1 Calcium upper bound)
#
# 79 GLY O 171 CA CA 2.8
#
  &rst iat= 1278, 2611, r3=2.8, r4= 3.3, ialtd=0, /
#
# 76 ASP OD1 171 CA CA 2.8
#
  &rst iat= 1247, 2611, r3=2.8, r4= 3.3, ialtd=0, /
#
# 77 GLY O 171 CA CA 2.8
#
  &rst iat= 1257, 2611, r3=2.8, r4= 3.3, ialtd=0, /
#
# 102 GLU OE2 171 CA CA 2.8
#
  &rst iat= 1585, 2611, r3=2.8, r4= 3.3, ialtd=0, /

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