Re: [AMBER] Problem with mdnab: ERROR in RATTLE

From: David A Case <>
Date: Wed, 18 Apr 2012 07:46:12 -0400

On Tue, Apr 17, 2012, case wrote:
> On Tue, Apr 17, 2012, Andrey wrote:
> > An archive with .prm/.crd/.pdb files produced by pytleap and minimized
> > .pdb files (in min/ directory) is available at
> > [].
> Thanks. I can certainly reproduce the error. I'm looking into this, and will
> report back if/when I figure out what is going on. (Others are of course
> welcome to debug as well!)

OK: the answer is remarkably simple: the peptide in cdk6_p6_3_cplx.leap.pdb
has many very long bonds (between all of its amino acids). Even after
minimization, you still have very bad bond lengths, which prevents rattle from

The cdk6_p6_1_cplx.leap.pdb file also has the same problem, but it is able to
minimize to a structure is good enough bond lengths to continue with rattle.

NAB makes this a bit hard to spot, since by default it combines the bond,
angle and dihedral into a single value, so you don't see the bond energy by
itself. Try adding the following lines before and after calls to conjgrad:

mme( x, f, -1);

where x[] and f[] are your coordinate and force arrays. This is will print
out details, and you can see that the bond energy for the "3" complex is much
higher than for the "1" complex.

Somehow, you will need to have better starting coordinates.

Finally, a rattle error should be fatal, and not let the program continue.
I'll update this and probably create a bugfix; but you can just add
"exit(1);" statements after the "Error in RATTLE" statements in rattle.c


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Received on Wed Apr 18 2012 - 05:00:03 PDT
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