Dear ccp4 community,
I started new approach appart from the primary idea writing
out trajectories *within* "the dynamics torsion function".
Now, writing trajectories *after* each "dynamics torsion function"
works fine for a simple movie-illustration! :o)
Special thanks to Dr. Gunnar Schroeder and Prof. Brunger for supporting me!
With best regards,
Sven
Here the solution:
___________________________
evaluate ($out_file = "out1SlowCool_" + encode($nmr.trial.count) +
".dcd")
write trajectory
output=$out_file
end
evaluate ($i_cool = 0)
while ($i_cool <= $ncycle) loop cool
evaluate ($i_cool = $i_cool + 1)
igroup
interaction (chemical h*) (all) weights * 1 vdw 0. elec 0. end
interaction (not chemical h*) (not chemical h*) weights * 1 vdw
$k_vdw end
end
if ( &md.type.cool = "torsion" ) then
dynamics torsion
cmremove=true
vscaling = true
tcoup = false
timestep = &md.cool.ss
nstep = $nstep
nprint = $nstep
temperature = $bath
end
else
dynamics cartesian
cmremove=true
vscaling = true
tcoup = false
timestep = &md.cool.ss
nstep = $nstep
nprint = $nstep
temperature = $bath
end
end if
write trajectory next end
if (&md.type.cool = "cartesian") then
evaluate ($radius=max($fin_rad,$radius-$rad_step))
parameter nbonds repel=$radius end end
evaluate ($k_vdw=min($fin_vdw,$k_vdw*$vdw_step))
else
evaluate ($k_vdw= $k_vdw + $vdw_step)
end if
evaluate ($bath = $bath - &md.cool.tmpstp)
@CNS_NMRMODULE:scalecool ( kdani=$kdani;
ksani=$ksani;
nmr=&nmr; )
end loop cool
write trajectory reset end
______________________________
Schünke, Sven schrieb:
Sorry I tried a lot:
The error-message is:
Program version= 1.2 File version= 1.2
MESSage=OFF
ECHO=FALSe {OFF}
TORMD: velocity rescaling (VSCAle) enabled
%VOPEN-ERR: > 99 versions present
%ASSFIL-ERR: error opening file out2_1.dcd
%ASSFIL error encountered: Error accessing file
(CNS is in mode: SET ABORT=NORMal END)
*****************************************************
ABORT mode will terminate program execution.
*****************************************************
Program will stop immediately.
With best regards,
Sven Schuenke
Dear ccp4 community,
I have a little problem during working with CNS (v1.21) and writing
trajectory files.
I would like to generate a simple movie during NMR structure calculation
steps (a simple visualization beginning from an extended protein strand
to the native fold according to NMR-constraints).
Therefore I tried to write trajectory-files during the calculation steps
(HT-phase, first slow-cooling and final energy-minimization phase).
However, CNS stopped after the HT-phase in the first
slow-cooling phase (writing trajectories in the HT-annealing stage
worked fine).
Error message:
____________________________________________________
Program version= 1.2 File version= 1.2
MESSage=OFF
ECHO=FALSe {OFF}
TORMD: velocity rescaling (VSCAle) enabled
%VOPEN-ERR: > 99 versions present
%ASSFIL-ERR: error opening file torsion_cooling_1.traj
%ASSFIL error encountered: Error accessing file
(CNS is in mode: SET ABORT=NORMal END)
*****************************************************
ABORT mode will terminate program execution.
*****************************************************
Program will stop immediately.
CNS has problems with writing out "trajectory"-files more than 99 files.
So, in each step CNS writes the following output-files:
out2_1.dcd
out2_1.dcd_1
out2_1.dcd_2...
...
out2_1.dcd_99
Is there any possibility to write trajectory files only in "one
single" file (like file-attaching for each step?) to overcome that problem?
This should be done in the annealing protocol section during the "first
slow cooling phase":
_____________________________________________________
evaluate ($out_file = "out2_" + encode($nmr.trial.count) + ".dcd")
if ( &md.type.cool = "torsion" ) then
dynamics torsion
cmremove=true
vscaling = true
tcoup = false
timestep = &md.cool.ss
nstep = $nstep
nprint = $nstep
temperature = $bath
trajectory= $out_file
nsavc=1
end
else
dynamics cartesian
cmremove=true
vscaling = true
tcoup = false
timestep = &md.cool.ss
nstep = $nstep
nprint = $nstep
temperature = $bath
end
end if
_____________________________________________________
But I do not know the exact "Expression/Syntax" to fix the problem.
Would you be able to help me please?
With best regards and thank you very much indeed,
Sven Schuenke
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Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt
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