The problem hasn't been solved
I'm using "rosetta_src_2017.36.59679_bundle". I'm trying to run the following bash script:
$ROSETTA_BIN/antibody.linuxclangrelease -fasta IGHab.fasta | tee grafting.log
I got following error:
[ERROR] EXCN_utility_exit has been thrown from: src/basic/execute.cc line: 55
ERROR: basic.execute encounter error while runnning blastp -db /short/wm35/rosetta/tools/antibody/blast_database/database.H2.20 -query grafting/h2.fasta -out grafting/h2.align -word_size 2 -outfmt 7 -max_target_seqs 1024 -evalue 2000 -matrix PAM30
Hello!
While using ddg_monomer script, I tried flag --ggd:dump_pdbs 'false' and 'true' both, but it is not producing any output pdb file? any suggestion?
"-ddg::dump_pdbs true # write out PDB files for the structures, one for the wildtype and one for the pointmutant for each iteration"
Thanks!
Malkeet
Hello!
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
Hello!
I am trying to truncate a CDR loop using remodel. I have previously used Rosetta version 58825.2016 (Score function:talaris2014) successful.
However I recently switched to rosetta weekly release:
"version": "rosetta.source.release-156", "week": 43, "year": 2017
And I am getting this error
protocols.forge.remodel.RemodelWorkingSet: (1) normal rebuild
core.kinematics.tree.Atom_: (1) [ FATAL ] old_atom not present in atoms list! 1
Hello,
I am trying to run a tutorail (rosetta-mdff-tutorial.pdf; 3.1 Structure prediction section) but I get an error during vmd -dispdev text -e fold_rpn11_terminus.tcl or more exactly during start_rosetta_abinitio rpn11_terminus rpn11_yeast_23-306_complete [list "resid 196 to 284"] 1 [list [list "rpn11_yeast_23-306_frag9" "rpn11_yeast_23-306_frag3"]] [pwd]/input $nstruct 0 0 0. Please see its log below.
Hi,
I am using the FastDesign protocol in RosettaScripts to design some residues in the neighborhood of a ligand, specifically with constraints of N-O pair distance for NAD binding.
I've added constraints for the two N-O pairs to be 3.0 and 3.3 angstroms each with harmonic function and sd of 0.5, but somehow the distances are not kept below ~4.0 at all. (I've just observed a structure with over 6.0 angstrom distances for the two pairs.
Hello!
While doing protein minimization, I found that the terminal amino acids of gap (let say 80 and 110) have incomplete valency e.g. -C(O) and -NH instead of -C(O)O-/H and NH2/H+ as rosetta consider them very neighbours during renumbering step.
I tried modifying both residues (let say 80 and 110) in different protein visualization plateforma and fed to Rosetta, but it modifies them to -C(O) and -NH.
Could you suggest how to deal with it?
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
Dear Rosetta community,
I am looking for a reason why my simulations stop before -nstruct is reached. This happens when I use rosettascripts.mpi.linuxgccrelease for some flexible docking. As many decoys don’t pass the Rosetta filters, I set -ntrials to 100.
And then, with:
-nstruct 500
-ntrials 100
I get exactly 500 decoys (which I anticipate), but for:
-nstruct 30 000
-ntrials 100