Dear Experts,
How do I write a netcdf file with VMD from a netcdf/dcd trajectory file?
It seems that VMD can read a netcdf file but cannot write it, as follows:
Info) Using plugin netcdf for coordinates from file /data1/Prathit/APP/OnlyAPP/AlphaFold2/770_res/Charmm-Gui_Dimer-units/E1-E1_3189357573/windows/smd.10_image.nc
Info) Coordinate I/O rate 139.6 frames/sec, 470 MB/sec, 3.6 sec
Info) Finished with coordinate file /data1/Prathit/APP/OnlyAPP/AlphaFold2/770_res/Charmm-Gui_Dimer-units/E1-E1_3189357573/windows/smd.10_image.nc.
1
vmd >
vmd > molinfo top get numframes
500
vmd > set nf [expr {[molinfo top get numframes]-1}]
499
vmd > set all [atomselect top all]
atomselect1
vmd > animate write dcd try.dcd beg 0 end $nf waitfor all sel $all
Info) Opened coordinate file try.dcd for writing.
Info) Finished with coordinate file try.dcd.
500
vmd >
vmd > animate write netcdf try.nc beg 0 end $nf waitfor all sel $all
ERROR) Unable to open file try.nc of type netcdf for writing frames.
vmd >
vmd > animate write netcdf try.nc type netcdf beg 0 end $nf waitfor all sel $all (basically it did not write an .nc file, unlike the generated .dcd file above)
vmd > ls
Any comments regarding the same will be deeply appreciated.
Thanks in advance.
Prathit Chatterjee
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