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Hydronmr - how to start

As a very beginner in using Linux/Python I didn't know why my downloaded lnx.exe didn't want to work. chmod command was the answer!

chmod stands for "change mode", and it is used to define the way a file can be accessed. the user can read, write, ande xecute it.

chmod u+x hydronmr...lnx.exe

Then, all you need is a file hydronmr.dat, like this example:

3.1-lysozyme                  !Name of molecule
lysozyme31-nmr                !Name for output file 
6lyz.pdb                      !Strucutural (PBD) file       
3.1,                          !AER, radius of the atomic elements
6,              !NSIG
1.0,            !Minimum radius of beads in the shell (SIGMIN) 
2.0,            !Maximum radius of beads in the shell (SIGMAX) 
293.,           !T (temperature, K)
0.01,           !ETA (Viscosity of the solvent in poises)
1,              !Iflag (dipoles)    
-2.7126         !Gyromagnetic ratio of N: unit: 10^7 rad.s^-1.T^-1
1.02            !N-H distance, angstroms
-160.           !Chemical shift anisotropy, ppm
3               !Number of values of magnetic field
14.09           !Magnetic field, teslas
11.74           !Magnetic field, teslas
7.05            !Magnetic field, teslas
*                             !End of file

Execute hydronmr now and the results will appear in .res file

Remember to change viscosity if you are working in different temperature than 293K
Etykiety:

Komentarze

  1. Unknown11 lutego 2020 23:56

    hi, my hydronmr file did not work, how to perform the .exe in linux?

    OdpowiedzUsuń
  2. betainverse24 kwietnia 2020 09:13

    I did that, but then got:

    open: can't stat file
    apparent state: unit 4 named hydronmr.dat
    lately writing direct unformatted external IO
    free(): invalid pointer
    IOT Trap
    Aborted (core dumped)

    OdpowiedzUsuń

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