The problem hasn't been solved
Hello,
Should the spanfile supplied to -in:file:spanfile option contain only the transmbrane helices or the trasnmembrane loops and sheets too?
Hi,
I am trying to convert a bunch of PDB files to silent files. Though I am successful in doing this with covert_silent and relax applications I still miss out Secondary structure information in the computed silent out file (every residue is defined as "L"). What I am actually looking for a way to obtain SS with its backbone dihedral angles of a given idealized pdb file. Is it even possible ? or I am missing any magical flag?
thanks,
Kala
Hi,
What would be a recommended number of structured generated for homology modeling. Most structures are close to the template. What do you think energy differences between clusters of the generated structures should be?
Thank you
I am going through the tutorial on how to add the NCAA's to Rosetta
on the example of ornithine. I managed to create the param file, and now
I am trying to create the rotamer library by using make_rot_lib application.
I noticed a strange behavior of the program for some values of phi and psi
angles. It works fine for the negative angles, but for some combinations of
positive angles I get errors. For instance for phi=40, psi=60, everything works fine,
but for phi=60, psi=40 I get a pdb file with two zeros in name instead of 60 and 40:
Hi, while running a homology model on Rosetta 3.4, I get an error
ERROR: Atom_::dihedral_between_bonded_children: atoms are not both my children!
ERROR:: Exit from: src/core/kinematics/tree/Atom_.cc line: 407
Any insights on why that might be?
Thank you.
Hello,
I'd like to ask few questions related to ddg_monomer application:
1) When I set number of iterations to 50 (-ddg::iterations 50), the average energy in ddg_predictions.out file does not correspond to the arithmetic mean of the individual runs in the full output file. When I set number of iterations to 20 (other settings is the same) everything is OK.
Hi,
I've tried to run rosetta docking with constraints. But in the output files it seems that only the first decoy fits the constraints while all the other decoys don't. Could someone help me figure this out?
My flags:
-s input/2ERK_06092.pdb
-ex1
-ex2aro
-docking_local_refine
-dock_pert 3 8
-spin
-nstruct 10
-no_filters
-constraints:cst_file input/distance_constraint
-out:overwrite
-out:file:fullatom
-out:file:scorefile score_dock.fsc
-out:file:silent decoys_dock.out
-mute core.io.database
-mute core.util.prof
My constraint file:
Sorry for this simple question. How to prepare a combined PDB file with two different PDB files? Thanks.
Hi,
I'm new to rosetta and trying to cluster 100 pdb structures using cluster and get a most common one. What should be the expected output files?
I read the cluster command user guide that the script need first 400 structures as the starting point, so is it because my 100 structures is too less, which cause the problem?
(https://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/d7/...)
I tried it twice:
A) my flag
-database /Applications/rosetta3.4/rosetta_database/
hi
i am running a kinematic loop modeling/design run but it keeps on crashing with segementation fault error. could you tell me how to avaoid this? thanks.
command line:
%loopmodel.gccrelease -database XXX @loopmodelflags
flagfile:
-loops:input_pdb XXX.pdb
-loops:loop_file XXX.loop
-loops:remodel perturb_kic
-loops:refine refine_kic
-loops:relax fastrelax
-loops:extended
-in:file:fullatom
-loops:max_kic_build_attempts 10000
-out:file:fullatom
-out:overwrite
-out:prefix AAA
-out:path ./
-out:file:scorefile score.sc
-ex1
-ex2
-nstruct 10000
-resfile XXX.resfile
