Dear all,
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
-------------- initialization---------------
| E(kin)+E(total)=36.310 E(kin)=0.022 temperature=7.356 |
| Etotal =36.288 grad(E)=0.094 E(VDW )=0.000 E(NOE
)=36.288 |
-------------------------------------------------------------------------------
%ATMCHK-ERR: unknown coordinates for atom " -1 -TOAC-TC :"
NaN NaN NaN
%ATMCHK-ERR: Unknown coordinates
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
BOMLEV= 0 reached. Program execution will be terminated.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Subroutine DIE called . Terminating
-------------------------------------------------------------------------------------------
This error usually occurs at the beginning of the rigid body dynamics.
Most of the time the program just continues, but at a certain point it
crashes.
I have found a similar question from an old post, but no solution was
provided:
http://www.bio.net/bionet/mm/x-plor/1996-January/000349.html
Any suggestions would be appreciated.
Best regards,
Jia-Ying Guan
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