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
>>
>> ------------------------------------------------------------------------------------------------
>> ------------------------------------------------------------------------------------------------
>> 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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