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I am seeking help with using MakeRotLib to generate a rotamer library for a new beta3–amino acid. I first created a parameter file using molfile_to_params_polymer.py and then manually edited it by renaming the backbone atom to CM and changing the related hydrogen atom names from HA to HM, following the naming conventions used for beta3–amino acids in the Rosetta database (e.g., B3D.params). After this, I prepared a rotlib_options.in file following the tutorial example (C40_rot_lib_options_XXX_YYY.in). The input file I am using is:
The protocol runs and performs minimization successfully, but it crashes while writing the rotamer library file. Below is the relevant verbose output immediately preceding the crash:
_protocols.make_rot_lib.MakeRotLibMover: ORIG ENER: 3.34304 MIN ENER: 0.418746 found in 8 steps
protocols.make_rot_lib.MakeRotLibMover: 180
protocols.make_rot_lib.MakeRotLibMover: 30
protocols.make_rot_lib.MakeRotLibMover: ORIG ENER: 5.59803 MIN ENER: 0.692167 found in 15 steps
protocols.make_rot_lib.MakeRotLibMover: Printing out log file to L13_180_180_180_180_180.mrllog...
protocols.make_rot_lib.MakeRotLibMover: Printing out rotamer library file to L13_180_180_180_180_180.rotlib...
protocols.jd2.JobDistributor: L13_0001 reported success in 1 seconds
*** Error in `/Computation/Rosetta-371/main/source/bin/MakeRotLib.static.linuxgccrelease':
double free or corruption (out): 0x000000003992daf0 ***_
I validated the parameter file using restype_converter, and the resulting SDF looks reasonable. I suspect the problem may be related to how I am defining the third backbone torsion (BB_RANGE), or to the CENTROID definitions for 2 CHI angles in the rotlib.in file.
I would greatly appreciate any guidance or suggestions on what might be wrong here.
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I am seeking help with using MakeRotLib to generate a rotamer library for a new beta3–amino acid. I first created a parameter file using molfile_to_params_polymer.py and then manually edited it by renaming the backbone atom to CM and changing the related hydrogen atom names from HA to HM, following the naming conventions used for beta3–amino acids in the Rosetta database (e.g., B3D.params). After this, I prepared a rotlib_options.in file following the tutorial example (C40_rot_lib_options_XXX_YYY.in). The input file I am using is:
AA_NAME L13
OMG_RANGE 180 180 1
PHI_RANGE XXX XXX 1
BB_RANGE YYY YYY 1
PSI_RANGE ZZZ ZZZ 1
EPS_RANGE 180 180 1
NUM_CHI 2
NUM_BB 3
CHI_RANGE 1 0 330 30
CHI_RANGE 2 0 330 30
CENTROID 300 1 180 2
CENTROID 180 2 300 1
TEMPERATURE 1
The protocol runs and performs minimization successfully, but it crashes while writing the rotamer library file. Below is the relevant verbose output immediately preceding the crash:
_protocols.make_rot_lib.MakeRotLibMover: ORIG ENER: 3.34304 MIN ENER: 0.418746 found in 8 steps
protocols.make_rot_lib.MakeRotLibMover: 180
protocols.make_rot_lib.MakeRotLibMover: 30
protocols.make_rot_lib.MakeRotLibMover: ORIG ENER: 5.59803 MIN ENER: 0.692167 found in 15 steps
protocols.make_rot_lib.MakeRotLibMover: Printing out log file to L13_180_180_180_180_180.mrllog...
protocols.make_rot_lib.MakeRotLibMover: Printing out rotamer library file to L13_180_180_180_180_180.rotlib...
protocols.jd2.JobDistributor: L13_0001 reported success in 1 seconds
*** Error in `/Computation/Rosetta-371/main/source/bin/MakeRotLib.static.linuxgccrelease':
double free or corruption (out): 0x000000003992daf0 ***_
I validated the parameter file using restype_converter, and the resulting SDF looks reasonable. I suspect the problem may be related to how I am defining the third backbone torsion (BB_RANGE), or to the CENTROID definitions for 2 CHI angles in the rotlib.in file.
I would greatly appreciate any guidance or suggestions on what might be wrong here.
Thank you,
Dammar
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