ADL: RMSD reference
home at unixdaemonuk.com
Wed Jan 21 03:11:36 PST 2009
Ruth Huey wrote:
> -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.
> Isabel Hilligerk wrote:
>> 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
>> 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
>> any molecule.
>> Isabel Hilliger.
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