ADL: RMSD reference

Kevin Wu kjwu at ucsd.edu
Tue Jan 20 12:52:15 PST 2009


Ruth,
Thanks for the clear explanation on RMSD in the dlg files. Is there anyway
to use rmsnosym keyword to recalculate the RMSD values in the dlg file?

Also, what was the intended use of the original implementation of RMSD in
autodock?

Thanks!

On Tue, Jan 20, 2009 at 9:52 AM, Ruth Huey <rhuey at scripps.edu> wrote:

> Hi,
>
> -In AutoDock, conformational clustering is performed after all the dockings
> have finished if the keyword |analysis| is given in the docking parameter
> file (DPF).
> -By default,  the atoms in the moving ligand (defined by the |move| keyword
> in the DPF) are used in the RMSD clustering calculations based on the
> tolerance defined by the |rmstol| keyword in the DPF.
> -If the |rmsref |keyword is in the DPF, the coordinates of the atoms in
> that file are used instead. Consequently, the file specified by the |rmsref
> |keyword must contain the same atoms in the same order as the file specified
> by the |move| keyword.
> -If the docking includes flexible residues, by default only the atoms in
> the moving ligand are used for the rmsd calculation.  If the |rmsatoms
> |keyword  is included in the DPF, the coordinates of the atoms in the
> flexible residues are also used for the rmsd calculation. In that case,  the
> file specified by the |rmsref |keyword must also contain the flexible
> residue atoms in the same order as the file specified by the |flexres|
> keyword.
>
> Please note that the rmsd calculation in AutoDock uses the distances
> between each atom in the docked structure and the nearest atom of the same
> element in the reference structure (instead of the distance between each
> atom and its equivalent in the reference structure) unless the |rmsnosym
> |keyword is in the DPF.
>    Ruth
>
>
> Isabel Hilligerk wrote:
>
>> Hi,
>>
>> Thank you for your previous help. I'm interested in reporting the results
>> i
>> have obtained with AutoDock. It seems that the RMSD reference value is an
>> interesting value to report because it indicates the success of the
>> docking
>> process. I would be very thankful if someone could explain me the use of
>> the
>> rmsref command. I also want to know which is the default reference
>> estructure used for the RMSD reference calculation when i haven't
>> specified
>> any molecule.
>>
>> Regards,
>>
>> Isabel Hilliger.
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>>
>>
>
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