ADL: too big RMSD

Christina Ha christina_triple_h at
Tue Dec 31 06:32:36 PST 2013


this is quoted from other mailing lists:
[Hi, as from the AutoDock 4.2 manual (page 38): rmsref <filename> (Optional) If included, the RMSD of the docked conformations will be calculated with respect to the coordinates in the PDB or PDBQT file specified here. This is useful when the experimentally determined complex conformation of the ligand is known. The order of the atoms in this file must match that in the input PDBQT file given by the move command. These values of RMSD will be output in the last column of the final PDBQT records, after the clustering has been performed. If this keyword is not included, the RMSD is calculated based on the starting position of the ligand. Stefano ]

This should mean co-crystalised ligand cannot be used as reference for RMSD of other test ligands.
Usually Reference RMSD for co-crystallised ligand is very low, only for new ligands it is very high due to the fact that Reference RMSD is calculated from initial position of the ligands which is not in the binding pocked. For instance, many compounds downloaded from pubchem has center coordinates around 0.000.

I've tried using Vina conformations as reference structure, managed to lower the Reference RMSD. 
Another way is to choose one of the conformations in DPF file, save as PDBQT, let AutoDock Tools use it as reference to re-calculate RMSD. This is mentioned in the manual for AutoDock Tools. (The way i do it is to visualize the conformations, and choose the one that binds the most similar way to the co-crystalized ligand) 

Date: Fri, 27 Dec 2013 02:59:38 -0800
From: ml-node+s1369657n7578341h13 at
To: christina_triple_h at
Subject: Re: ADL: too big RMSD


rmsd calculation should be done with cocrystalised ligand as reference. from the pdb save the ligand file as pdbqt and without altering any coordinates use this file for rmsd calculation

With Regards,


Vadiraj Kurdekar,

Research Scholar, Pharmacy Dept.,

Birla Institute of Technology and Science-Pilani,

Pilani Campus, 

Rajasthan, PIN: 333031



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On Wednesday, 25 December 2013 12:14 AM, Christina Ha <[hidden email]> wrote:


Eiichi AKAHO wrote

> Dear AutoDockers:


> In the AutoDock4, we can specify the reference structure of RMSD

> calculation by 

> using the rmsref command with reference structure as in the below.


> rmsref   1t64_key.pdbqt              # ref structure of rms calculation


> The  autodock4.exe result (output .dlg file) , however, shows very big

> RMSD values such as

> 60 to 100 A, although the docked inhibitors are well superimposed with

> ref. structure.


> RMSD should be 1- 5 A in this case. Why do I get very big RMADs?

> Anyone's help is very much appreciated.


> Thanks.


> Eiichi


> ////////////////////////////////////////////////////////////////////////

> 神戸学院大学薬学部物性薬学部門(Division of Physical Pharmacy,

> Faculty of Pharmaceutical Sciences, Kobe Gakuin University)

> 赤穗榮一 (Eiichi AKAHO)

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> ________________________________________________

> --- ADL: AutoDock List  ---
Hi. I'm a new AutoDock user.

I'm docking new ligands into a protein from pdb. Tried a couple of runs and

managed to get a low reference RMSD by altering the DPF file. Here's what I


move Inosine.pdbqt                     # small molecule

about 0.3242 0.1958 -0.0818          # small molecule center

tran0 4.58 20.738 21.443             # initial coordinates/A or random

-----> set it as center coordinates of the co-crystallized ligand.

rmsref inosine.pdbqt      # ref structure of rms calculation ------> insert

this line right after tran0, putting it in the very last line wont work.

I'm using the best affinity model in the Vina output file as my rmsref.

Hope this helps, and do point out if there's any mistake.



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