[Dock-fans] problem related to rmsd

[Scott Brozell]

Hi,

On Tue, Apr 28, 2009 at 03:05:50PM +0530, shalu jhanwar wrote:
> 
> 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 ?

http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#LigandFileInput
calculate_rmsd [no] (yes, no):
#Flag to calculate the heavy atom RMSD between the final ligand pose
#and its initial structure.

> 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?

Are you sure it is not in a file like this, eg,
dock6/install/test/ligand_io/io4_scored.mol2.save

########## Name:     ZINC00003959
########## RMSD:     0

@<TRIPOS>MOLECULE
...

Scott