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

From: Andrey <>
Date: Mon, 23 Apr 2012 12:25:56 +0400

On 04/18/2012 03:46 PM, David A Case wrote:
> 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
> converging.
> 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
> ...regards...dac
Thank you very much!
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Mon Apr 23 2012 - 01:30:03 PDT
Custom Search