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enzdes error

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enzdes error

I'm trying to learn enzdes using tutorials in demo and in the paper "de novo enzyme design using rosetta3". The first several steps went well, but when I tried the actual design step, I got this error: ERROR: Illegal value for real option -enzdes:cut1 specified: 6.0. This does not make sense at all. Anyone can help with this? Thanks.

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Tue, 2012-08-21 09:12

What does your command line and flags file look like?

Tue, 2012-08-21 11:16

Here are the flags I used:
-s UM_1_E41H272K271_1TML_mocktim_1.pdb
-extra_res_fa 1n1.params
-enzdes:cstfile mocktim.cst
-enzdes:cut1 6.0    
-enzdes:cut2 8.0     
-enzdes:cut3 10.0      
-enzdes:cut4 12.0  
-enzdes:design_min_cycles 3
-enzdes:lig_packer_weight 2
-packing:linmem_ig 10  

Here is the command line:
rosetta3/rosetta_source/bin/enzyme_design.linuxgccrelease -database ~/rosetta3/rosetta_database/ @tim.flags

Tue, 2012-08-21 13:29

I don't know why you're getting that error. The best I can come up with is that there is some sort of invisible/non-printing character after the "6.0" which is confusing the options reader. My suggestion would be to re-type the flags file (*don't* copy & paste, lest you copy & paste the non-printing character) and retry it.

Wed, 2012-08-22 11:17

Thank you very much for your great help, Rocco! I rewrote the flag file and it works now. It's definitely an error caused by some invisible characters.

Wed, 2012-08-22 13:32