modeller_usage May 2024

modeller_usage@salilab.org

2 participants
2 discussions

coarse parallelization
by Jed Goldstone 16 May '24

16 May '24

I would like to use coarse-grained parallelization with automodel (through slurm) to create (say) 100 models. As Modeller is deterministic, even if I start a job array with different model numbers, each separate job creates the same models. So, for example, if I start job using 4 different python scrips with model ids 0-24, 25-49,50-74, and 75-99, I will get 4 sets of identical models. How can I turn off this deterministic behavior? With thanks, Jed . . Jed Goldstone, PhD Biology Department Woods Hole Oceanographic Institution

2 1

_modeller.ModellerError: getpdf__389E> MDT table range is too small. MDT should be derived with the full range of possible values for the independent variables.
by Rana Rehan Khalid 06 May '24

06 May '24

Dear Modeller Users, I am currently attempting to generate various mutant models using the MutantBuilder script available at https://github.com/eved1018/MutantBuilder. I have installed Modeller10.5 for this purpose. However, I am encountering the following issue: python3 MutantBuilder.py -pdb complex.pdb -c B Traceback (most recent call last): File "/home/rehan/Downloads/MutantBuilder-master/MutantBuilder.py", line 372, in <module> main() File "/home/rehan/Downloads/MutantBuilder-master/MutantBuilder.py", line 368, in main model(pdb, mutants, chain, mutant_name, outfolder) File "/home/rehan/Downloads/MutantBuilder-master/MutantBuilder.py", line 188, in HomologyModel mutant_pdb = autoModelPDB(pdb, aln ) File "/home/rehan/Downloads/MutantBuilder-master/MutantBuilder.py", line 204, in autoModelPDB a.make() File "/home/rehan/miniconda3/lib/python3.10/site-packages/modeller/automodel/automodel.py", line 141, in make self.homcsr(exit_stage) File "/home/rehan/miniconda3/lib/python3.10/site-packages/modeller/automodel/automodel.py", line 638, in homcsr self.mkhomcsr(Selection(self), aln) File "/home/rehan/miniconda3/lib/python3.10/site-packages/modeller/automodel/automodel.py", line 716, in mkhomcsr self.build_charmm_restraints(atmsel, rsr, aln) File "/home/rehan/miniconda3/lib/python3.10/site-packages/modeller/automodel/automodel.py", line 678, in build_charmm_restraints rsr.make(atmsel, aln=aln, restraint_type=type+'_dihedral', File "/home/rehan/miniconda3/lib/python3.10/site-packages/modeller/restraints.py", line 156, in make return func(self.__mdl.modpt, edat.modpt, aln.modpt, io.modpt, _modeller.ModellerError: getpdf__389E> MDT table range is too small. MDT should be derived with the full range of possible values for the independent variables. Could someone please assist me in resolving this problem? Your help would be greatly appreciated. Best Wishes Rehan

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modeller_usage May 2024