From: Ross Walker <>
Date: Wed, 10 Jan 2007 09:17:11 -0800

Dear Steve,
The close contact warning in xleap is a little over zealous in the number of
things it considers to be a close contact. Start by going through all the
close contacts and look for any which are very close. I.e. less than half an
angstrom or so. These will be the real problematic ones since minimization
is unlikely to correct them. Ones that are just a little bit too close will
normally get fixed by the minimization. Note, if run the check command after
adding waters you will get a crazy number of close contacts, pretty much all
of which can be ignored.
Anyway in terms of minimization strategy use sander to do the minimization
(don't try using Leaps relax). Try doing just 500 steps of steepest descent
first of all without restraints. It would be useful to see the output from
this run. In particular what the maximum gradient is early on and which atom
has the most force on it. If you get linmin failures very early on here or
the maximum force stays very large then you may need to try some other
One thing you could do is locate where the worst offenders are and use belly
to fix everything but these atoms and the atoms around 4 to 5 atoms up the
chain from then. Then repeat the minimization for 50 steps or so. Then
remove more of the belly mask and rinse repeat until the change in the
structure looks good. If you find that minimization doesn't solve the
problem what you could do is try some very low temperature MD.
Again belly the atoms that look to be okay so that just the bad contacts and
immediate surroundings can move. Then try setting up a 100 step long MD run
with tempi=0.0 and temp0=10.0 - I.e. only 10K max with ntt=3 and
gamma_ln=0.5 or so (you may also want to try a high gamma_ln value of say
10.0 or so if you find the huge potential energy suddenly dumps into kinetic
and the temperature spikes to a very high value above temp0). Also set the
timestep very small say 0.1fs (dt=0.0001). Do not use shake at this point.
Also set ntpr=1 and ntwx=1. This way you can watch the trajectory in a
visualization program and see how it progressed. With several cycles of this
type of approach, increasing the number of steps to say a 1000 or so and
slowly raising the temperature in stages to say 50K as you release the belly
mask. Then you can slowly raise the timestep, turn on shake and after a
while you should be good to ultimately remove belly all together and start
running a proper heating and equilibration run.
All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
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From: [] On Behalf Of
Steve Seibold
Sent: Wednesday, January 10, 2007 08:46
Subject: AMBER:

Hello Amber

I have a crystal structure of a large enzyme (resolution ~ 2.5Angstroms).
When up load my structure (without hydrogens) in to xleap, xleap then adds
hydrogens to my structure. However, it then tells me when I do a "check"
unit that the hydgrogens it has added are "Warning: Close Contact" between
atoms of the protein and the hydrogens it has added. There are 170 warnings
of this kind. I have tried to energy minimize the structure, but it is
proving to be very, very difficult with the repeat warning (in sander during
minimization) "repeated limit failure" and stops the minimization. I have
tried every routine (i.e. different strategies for minimization..i.e.
different ncycle and maxcycle) and nothing is working. Can you some one give
me some advice?


Thanks, Steve



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Received on Sun Jan 14 2007 - 06:07:11 PST
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