Error with GB

From: Jarrod Smith <>
Date: Tue 21 Mar 2000 12:33:26 -0600

I'm trying to run an NMR refinement of a drug-DNA system with igb=1 in
AMBER6. Here is the &cntrl namelist input:

    nstlim=20000, pencut=0.02, nmropt=1,
    ntpr=250, ntt=1, ipnlty=1, igb=1, vlimit=10,
    scee=1.2, ntb=0,

When I set igb=3 in the above, the calculation runs fine. With igb=1,
sander immediately exits with no messages to stderr or stdout. The last
couple lines of mdout say:

Using modified Bondi radii and Tinker screening parameters
 Unable to find bonded partner for atom 737

I'm assuming this is why the calculation dies. I looked at atom 737 and
there seems to be nothing strange here. It is a proton attached to a
carbon atom in the minor groove binding drug that I am studying. The
only non-standard thing I can think of with this system is that the drug
is crosslinked to the DNA. But atom 737 is not involved. I made an
bond file with the -bnd option of ambpdb to check and see if the bond to
atom 737 is in the prmtop file. It is, and just for good measure the
crosslink is there, too.

Any ideas?

Jarrod A. Smith, Ph.D.
Assistant Director, Center for Structural Biology
Molecular Graphics and Computation
Received on Tue Mar 21 2000 - 10:33:26 PST
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