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

From: case <>
Date: Sat, 14 Apr 2012 14:04:34 -0400

On Fri, Apr 13, 2012, Andrey wrote:
> However, when I try to run subsequent equilibrium with mdnab, for 2 of 8
> complexes I encounter the following error:
> mdnab "../min/pdb/${PREFIX}.pdb"
> "../../build/amber/${PREFIX}.leap.prm" "traj/${PREFIX}" 2 500
> Reading parm file (../../build/amber/cdk6_p6_3_cplx.leap.prm)
> iter Total bad vdW elect nonpolar
> genBorn frms
> ff: 0 -7285.90 4577.15 -1029.51 -6770.49 0.00 -4063.05
> 3.53e-01

> For other complexes besides these two (even the ones with the same
> peptide, but another binding point) mdnab finishes successfully.

This is indeed odd. I'm assuming that the nab tests (especially Run.rattle)
passed. You might try a test run in dt=0.001 to see if that helps. Also
set ntpr_md=1 so that you can see the most information (just run a few steps,
since it basically goes haywire at the first step.)

Otherwise, I think you will have to post examples of a job that works and one
that fails. The minnab and mdnab codes are fairly new, and only a few people
are using them, so there could well be hidden problems lurking.

Also let us know what version of AmberTools you are using, and which compiler
and OS.


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Received on Sat Apr 14 2012 - 11:30:03 PDT
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