From: Steve Seibold <>
Date: Wed, 10 Jan 2007 14:03:30 -0500

Thanks Ross for the ideas.

I am in the process of trying them now.


Cheers, Steve



From: [] On Behalf
Of Ross Walker
Sent: Wednesday, January 10, 2007 12:17 PM
Subject: RE: AMBER:


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 tricks.


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 |
| Tel: +1 858 822 0854 | EMail:- |
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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 - 06:07:13 PST
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