VMD-L Mailing List

From: Prathit Chatterjee (pc20apr_at_REMOVE_yahoo.co.in)
Date: Thu Dec 23 2021 - 05:00:44 CST

Dear Experts,Kindly let me know how to 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.ncInfo) Coordinate I/O rate 139.6 frames/sec, 470 MB/sec, 3.6 secInfo) Finished with coordinate file /data1/Prathit/APP/OnlyAPP/AlphaFold2/770_res/Charmm-Gui_Dimer-units/E1-E1_3189357573/windows/smd.10_image.nc.1vmd >vmd > molinfo top get numframes500vmd > set nf [expr {[molinfo top get numframes]-1}]499vmd > set all [atomselect top all]atomselect1vmd > animate write dcd try.dcd beg 0 end $nf waitfor all sel $allInfo) Opened coordinate file try.dcd for writing.Info) Finished with coordinate file try.dcd.500vmd >vmd > animate write netcdf try.nc beg 0 end $nf waitfor all sel $allERROR) 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 > lsAny comments regarding the same will be deeply appreciated.Thanks in advance.Prathit Chatterjee