ADL: RMSD

bagdevi.mishra at gmail.com bagdevi.mishra at gmail.com
Wed Apr 22 05:03:39 PDT 2009


after getting the dlg file you can run the python code summarize_results4.py


It has following options.

Usage: summarize_results4.py -d directory

    Description of command...
         -d     directory
    Optional parameters:
        [-t]    rmsd tolerance (default is 1.0)
        [-f]    rmsd reference filename
        (default is to use input ligand coordinates from docking log)
        [-b]    print best docking info only (default is print all)
        [-L]    print largest cluster info only (default is print all)
        [-B]    print best docking and largest cluster info only (default is
print all)
        [-o]    output filename
                      (default is 'summary_of_results')
        [-a]    append to  output filename
                      (default is to open output filename 'w')
        [-k]    build hydrogen bonds and report number built
        [-e]    compute estat, vdw, hb + desolv energies and report
breakdown
        [-r]    receptor filename
        [-u]    report unbound energy
        [-i]    subtract internal energy
        [-p]    report depth of torsion tree
        [-v]    verbose output




On Wed, Apr 22, 2009 at 3:56 PM, kannan cham <kannan_cmn at yahoo.co.in> wrote:

> Hi
>
> Can anyone tell me how to find the RMSD after the docking.... and also
> tell me what is the range of the RMSD values....Thank you..
>
>
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