Unable to run stride function
I'm trying to run the stride function. According to your instructions I've put the stride executable found in VMD in the folder containing the pdb file that I want to examine. I first run the pdb.read function to import the pdf file and then run the stride function as follows.
SOApo <- read.pdb("SeaOtterApoA1Dimer.pdb") stride(SOApo, exefile = 'C:/Users/tig_m/Documents/Thesis project/Computational experiments/PyMod models/Sea Otter Apo A-I/Lipid Free Structure/stride_WIN32.exe', resno = TRUE)
I don't understand why R is not able to to recognize the file path to the stride executable. I get the following error message:
'C:/Users/tig_m/Documents/Thesis' is not recognized as an internal or external command, operable program or batch file. Error in file(con, "r") : cannot open the connection In addition: Warning messages: 1: In shell(paste(exefile, " -f", outfile, " ", infile, sep = "")) : 'C:/Users/tig_m/Documents/Thesis project/Computational experiments/PyMod models/Sea Otter Apo A-I/Lipid Free Structure/stride_WIN32.exe -fC:\Users\tig_m\AppData\Local\Temp\RtmpCu6K8O\file197c120d124a C:\Users\tig_m\AppData\Local\Temp\RtmpCu6K8O\file197c653d31dd' execution failed with error code 1 2: In file(con, "r") : cannot open file 'C:\Users\tig_m\AppData\Local\Temp\RtmpCu6K8O\file197c120d124a': No such file or directory
I would be very grateful for your help on this because I'm not sure what it's attempting to read a different file path.
Comments (3)
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Not a bug
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Hi,
You need to add quotation marks if a path name contains space. For example,
stride(…, exefile='“C:/XXX/prog loc/stride.exe”')
. Try and see if it works.