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

King Zhang shuxing at bioanalysis.org
Thu Oct 13 15:03:06 PDT 2005

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


"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


Thank you very much!





King Zhang, Ph.D

Research Scientist

Building 244, Rm 116

Biotechnology HPC Application Institute

Fort Detrick, MD 21702

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