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Ligand dock analysis

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Ligand dock analysis

Hi all,

I am running ligandDocking application thru rosetta_scripts app. On the documentation "Rosetta Ligand Docking with Flexible XML Protocols", there is a paragraph addressing how to analyse the result.
The example can be downloaded from "" in the supplement info.
I did exactly what it says on the example folder provided in the documentation but there is error relating to the residue type:

ERROR: Attempting to add a residue type with name 'CP1' but this name is already taken.
Please check your residue parameter files.

ERROR:: Exit from: src/core/chemical/ line: 389
application called MPI_Abort(MPI_COMM_WORLD, 911) - process 0

The command I gave was:

rosetta_scripts.linuxgccrelease -database $ROSETTA_DATABASE @flags -parser:protocol extract.xml -in:file:atom_tree_diff atom_tree_diff -in:file:extra_res_fa inputs/7cpa.params

Have I missed out anything?

I could be simply outputting the results into and pdb files, but if I want to output like 10000 models that would be a pain. Please help~

Post Situation: 
Tue, 2012-05-22 01:20

The error indicates that CP1 is getting loaded twice. Is CP1.params (perhaps 7cpa.params, I don't know) already in your @flags file? If it's in both the flags file already and you added it on the command line, it will try to load twice and get this error. It might also be that it's already in your database somewhere (it doesn't appear to be in my copy of 3.4).

Tue, 2012-05-22 06:51

Ahhh!!! right~ it really solve the whole problem! Thanks!

Tue, 2012-05-22 08:16

Usually this occurs when (as mentioned above) you have the same params file specified in the flags file and on command line. If you are still struggling with this, you can attach your flags file, params file, and input PDB, and mention the version of Rosetta you are using and I can have a look at it.

Tue, 2012-05-22 08:18