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recently I have tried to dock some different peptides to binding pocket of protein kinase and see their performance in flexpepdock. In the meanwhile I also dock some random peptides, such as poly G (GGGGGSGG) and poly E peptide(EEEEESEE). Interestingly, the energy score of good peptides and random peptides didn't show much differences(from -650 to -690), sometimes the random peptides even showed the better energy score. In order to keep them in the pocket I have made some constraint. The orientation of peptides are similar.
I am trying to find the residues interacting with a particular residue of interest so as I can determine which residue-residue interaction is making the most contribution to a specific scoring term. However, I have not been able to find the residue_pair_energy function.
Do I need to write the function class to obtain this or is there a function that already available (e.g. to get atom-atom pairwise energies). If the latter case where is the function located.
I have tried core.scoring.Energies but it does not exist there
I'm using "rosetta_src_2017.36.59679_bundle". I'm trying to run the following bash script:
#!/bin/bash $ROSETTA3/home/labusr/rosetta/main/source/bin/score_jd2.macosclangrelease \ -database $ROSETTA3/database/ \ -database ~/Rosetta/database/ \ -in::file::s /home/labusr/Documents/1issA.pdb \ -ignore_unrecognized_res \ -edensity::mapfile /home/labusr/Documents/1issA_6A.mrc \ -edensity::mapreso 5.0 \ -edensity::grid_spacing 2.0 \ -edensity::fastdens_wt 35.0 \ -beta \ -edensity::cryoem_scatterers \ -crystal_refine
Can anyone point me to good examples of implmentations for setup_for_packing and prepare_rotamers_for_packing (and I guess update_residue_for_packing while I'm at it)? I'm not entirely sure I understand what the arguments are for these methods and the use case for when I would want to implement these methods.
Thanks in advance!
I have created an energy method and it works. However, I want to do a check at the time it is created for whether a particular score_type is enabled. Is there any way to know which score_types are enabled from within my create_energy_method function?
I am attempting to use Rosetta 3.8 (2017.29.59598) AbinitioRelax with some constraints I have defined, but I get the feeling that the constraints are not being properly implemented. In particular, I attempt to implement a single harmonic constraint using a constraint file with this line:
AtomPair CA 1 CA 41 HARMONIC 55.0 .1
My flags are:
I am trying to use the packstat application for measuring the quality of my model. But, I'm not sure what the terms in output mean? (there is no info in user guide/documentation). I came up with the flags I've used from the RosettaHoles2 paper. As per the paper, it should output some pdb and also output explicit representation of voids. But, I donot see any output files. I only get the commandline output with three score columns.
Could someone clarify?