From: Efthymiou, Christos (
Date: Tue Nov 08 2022 - 12:06:45 CST


I would like to run PCA analysis on a NAMD .dcd simulation, but I am having trouble with ProDy in the Normal Mode Wizard. I am using VMD 1.9.4a53 on a Windows 10 computer.

I started VMD, loaded my PSF and DCD files, and then opened the NMWiz plugin. I then clicked the ProDy interface and changed the ProDy job to a PCA calculation, and changed the output directory to my downloads folder. I left all the other settings as their default values. Once I clicked submit, I was prompted to designate the path to the ProDY executable file, which I did.

However, at the execution stage, I get an error regarding an invalid NMD file path. Here is what is printed in the VMD console for all the steps I described above:

vmd > psfplugin) Detected a Charmm PSF file
Info) Using plugin psf for structure file R:/Wildtype_100ns_Test1/Wildtype_100ns_Test1/run/Wildtype_100ns_Test1_QwikMD.psf
Info) Analyzing structure ...
Info) Atoms: 75710
Info) Bonds: 52672
Info) Angles: 35117 Dihedrals: 17815 Impropers: 1145 Cross-terms: 415
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 23538
Info) Waters: 22984
Info) Segments: 11
Info) Fragments: 23121 Protein: 2 Nucleic: 0
dcdplugin) detected standard 32-bit DCD file of native endianness
dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
Info) Using plugin dcd for coordinates from file R:/Wildtype_100ns_Test1/Wildtype_100ns_Test1/run/MD.dcd
Info) Coordinate I/O rate 1.05 frames/sec, 0 MB/sec, 9.5 sec
Info) Finished with coordinate file R:/Wildtype_100ns_Test1/Wildtype_100ns_Test1/run/MD.dcd.
Info) Opened coordinate file C:/Users/Christos/Downloads/Wildtype_100ns_Test1_QwikMD_psf_pca.dcd for writing.
Info) Finished with coordinate file C:/Users/Christos/Downloads/Wildtype_100ns_Test1_QwikMD_psf_pca.dcd.
Info) Opened coordinate file C:/Users/Christos/Downloads/Wildtype_100ns_Test1_QwikMD_psf_pca.pdb for writing.
Info) Finished with coordinate file C:/Users/Christos/Downloads/Wildtype_100ns_Test1_QwikMD_psf_pca.pdb.
Info) 10 frames are written as C:/Users/Christos/Downloads/Wildtype_100ns_Test1_QwikMD_psf_pca.dcd
Info) Executing: C:/Users/Christos/AppData/Local/Programs/Python/Python39/python.exe C:/Users/Christos/Desktop/prody.exe pca --quiet -s all -o "C:/Users/Christos/Downloads" -p "C:/Users/Christos/Downloads/Wildtype_100ns_Test1_QwikMD_psf_pca" -n 10 "C:/Users/Christos/Downloads/Wildtype_100ns_Test1_QwikMD_psf_pca.dcd" --pdb "C:/Users/Christos/Downloads/Wildtype_100ns_Test1_QwikMD_psf_pca.pdb"
ERROR) C:/Users/Christos/Downloads/Wildtype_100ns_Test1_QwikMD_psf_pca.nmd is not a valid NMD file path.

Is it necessary to create an NMD file prior to performing a PCA calculation with the ProDy interface in the Normal Mode Wizard? If so, how would I do this? I appreciate any guidance on solving this issue as I am not sure if I have missed any necessary steps to make this work properly.