MakeRotLib

[Anonymous]

I have a about MakeRotLib quenstion:

when I run $ROSETTA3/bin/MakeRotLib.static.linuxgccrelease -database $ROSETTA3_DB -options_file C40.in，Error is as follows：

basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv

basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv

basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv

basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv

basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv

core.chemical: [ WARNING ] protein residue C40 is not explicitly listed as either L or D in its params file.

core.chemical: [ WARNING ] To avoid seeing this warning in the future, add “L_AA”, “D_AA”, or “ACHIRAL_BACKBONE” to the “PROPERTIES” line of the params file.

core.chemical: [ WARNING ] protein residue Dap is not explicitly listed as either L or D in its params file.

core.chemical: [ WARNING ] To avoid seeing this warning in the future, add “L_AA”, “D_AA”, or “ACHIRAL_BACKBONE” to the “PROPERTIES” line of the params file.

core.chemical: [ WARNING ] protein residue Cit is not explicitly listed as either L or D in its params file.

core.chemical: [ WARNING ] To avoid seeing this warning in the future, add “L_AA”, “D_AA”, or “ACHIRAL_BACKBONE” to the “PROPERTIES” line of the params file.

ERROR: dont add residue bonds more than once!

ERROR:: Exit from: src/core/chemical/ResidueType.cc line: 1448

BACKTRACE:

[0x5d62318]

[0x57a6345]

[0x5761914]

[0x57669fd]

[0x56f37b0]

[0x56fefb3]

[0x56e7224]

[0x56e9b17]

[0x56e8b1c]

[0x4454a21]

[0x445514b]

[0x44d575c]

[0x44e6036]

[0x44db2c5]

[0x48e163b]

[0x44d7194]

[0x44a2ace]

[0x44a7967]

[0x44a9366]

[0x44a95cb]

[0x44bf7da]

[0x44c04a2]

[0x44c0ce2]

[0x1d7db94]

[0x627b3a]

[0x4118a8]

[0x625a934]

[0x62741d]

caught exception 

File: src/core/chemical/ResidueType.cc:1448

[ ERROR ] UtilityExitException

ERROR: dont add residue bonds more than once!

 

 

[Anonymous]

The problem is somewhere in your noncanonical amino acid’s params file.  You’ve got duplicated bonds declared between atoms in the residue.

[Anonymous]

Hi
I am trying to convert a mol2 file to params file using mol2genparams.py script. The mol2params conversion appears to work (please see attached log file) but when I run rosetta_scripts to perform GAliganddocking, it throws up an error “dont add residue bonds more than once”. I have looked at the params file but can’t see any obvious duplications. I am following the protocol outlined for generating mol2 file for GAliganddocking at this location. https://www.rosettacommons.org/docs/latest/GALigandDock-Preprocessing

The .params file is uploaded as a txt file. I would deeply appreciate any help. I have been at it for a week and just can’t seem to find a work around. I have tried to generate mol2 file from different sources, also tried starting from SMILES, pdb and mol but ended up with the same result.

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