[Dock-fans] How to Use RMSD command from DOCK5

Terry Lang terry at cgl.ucsf.edu
Fri Oct 14 17:12:50 PDT 2005

Dear King,

There are two problems with what you are doing. First, DOCK can only 
read .mol2 or mulit-mol2 format. You need to convert your pdb files into 
mol2 for DOCK to be able to load them. Second, the rmsd function only 
works between the same ligand at different orientations. You need to 
have the same molecule as reference for the rmsd calculation as is being 
docked for it to work.


King Zhang wrote:

> Dear DOCK experts:
> I was trying to use RMSD accessory command from DOCK5 to calculate the 
> RMSD between multiple ligands and a reference ligand but failed. Does 
> any one happen to know the format of the second file (the comparison 
> file)? Based on the information provided for RMSD command, I 
> concatenated multiple pdb files into one file and then used it as the 
> second file. The error is like the following:
> “Error! Atom count discrepancy: 30 120”.
> I have 4 ligands in the second file.
> If you could let me know how to solve the problem, I would highly 
> appreciate it!
> Thank you very much!
> King
> King Zhang, Ph.D
> Research Scientist
> Building 244, Rm 116
> Biotechnology HPC Application Institute
> Fort Detrick, MD 21702
>Dock-fans mailing list
>Dock-fans at docking.org

P. Therese Lang
Kuntz and James Labs
UCSF--Chemistry and Chemical Biology
Phone: (415)476-3986


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