Hello Jia-Ying--
>
> I am trying to dock a protein with a pseudoatom of a TOAC radical
> with rigid body dynamics. Below is the section for rigid body
> dynamics in my script:
> ------------------------------------------------------------------------------------------
> vector do (fbeta=0.06) (name TC)
> vector do (vx=0.0001)(name TC)
> vector do (vy=0.0001)(name TC)
> vector do (vz=0.0001)(name TC)
>
> dynamics rigid
> nstep=100
> dt=0.0001
> group=(name TC and resi 1)
> dynmode=TCOU
> tbath=300
> nprint=100
> NTRFRQ=0 !new for XPLOR vs 3.8
> end
> ------------------------------------------------------------------------------------------
>
> There is one error that I could not find the solution to solve (see
> below).
>
> ------------------------------------------------------------------------------------------
> %RIGMD3-ERR: inconsistent qs 0.000000000000000E+000
> 0.000000000000000E+000
> 0.000000000000000E+000 0.000000000000000E+000 -1.00000000000000
> 0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
> -1.00000000000000 NaN NaN
> NaN NaN NaN
> NaN NaN NaN
> NaN
Looking at the source, I see that this indicates an inconsistent
rotation matrix corresponding to the first 9 numbers. A simplest first
approach would be to switch over to using the internal variable
module, accessible in the old XPLOR interface using the dynamics
internal statement. If you have similar problems with the IVM, we can
investigate further.
best regards--
Charles
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--
Charles Schwieters email: Charles at Schwieters.org
www: http://schwieters.org/cds
phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt
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