# MakeRotLib

3 posts / 0 new
MakeRotLib
#1

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!

AttachmentSize
924 bytes
Post Situation:
Fri, 2019-07-26 02:18
yinasun

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

Fri, 2019-07-26 15:00
vmulligan

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.

File attachments:
Sun, 2020-04-12 08:01
jalan