[Dock-fans] problem related to rmsd

[shalu jhanwar]

Hi everyone ,

I have done virtual screening .In rigid.in file (a input file for docking) ,
i have given
calculate_rmsd                                               yes
use_rmsd_reference_mol                                no

I have not given any reference molecule .Which molecule it is considering
and calculating rmsd ?

I have also done another experiment .I have given a reference molecule ,the
original ligand of the receptor .But this molecule is not present in NCI
dataset (virtual screening dataset) .At this time it is not calculating rmsd
in the output file during docking .Why?

Kindly give me reasons .
Thank you.
Waiting for your replies .


Shalu Jhanwar
M.Sc Bioinformatics
Banasthali University
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