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Flexible backbone design using PSSM


Currently I am running Rosetta flexible backbone design (ver. 3.3) to create novel proteins. My problem is, when I add PSSM as a favourable sequence profile, sometimes negative/positive weights behave strangely. The below is my XML code.

[Reweight scoretype=res_type_constraint weight=1.0/]

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RosettaVIP: ERROR: seqpos <= size()

Hi, I tried RosettaVIP shipped in Rosetta3.4. In some cases it breaks after a few iterations with this error: ERROR: seqpos I can not figure out the root for the error from the source file. The command line I used is: vip.linuxgccrelease -s mypdb -cp:cutoff 6.0 -sasa_calculator_probe_radius 1.0 -cp:output myoutput -cp:print_reports -run:silent I have not observed other anomalies in the screen printout before the ERROR, neither in the reports.txt file.
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problems with low-resolution loop refinemet (LoopMover_Perturb_CCD)


I am trying to replicate some of the examples of the PyRosetta manual and tutorial. I have several problems with the LoopMover_Perturb_CCD. See the code below

1) I am getting the same conformation 10 times (instead of 10 different conformations). Conformations looks the same and have the same energy. Is LoopMover_Perturb_CCD not properly working in PyRosetta or what I am doing wrong?

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how to repacking loop while freezing other residues?


I rebuilded two missing loops in a crystal structure and tried to use Rosetta to refine these loops. I want to refine the loops but keep the rest of the native structure (both backbone and side chain) "freeze". However,each time the loops were repacked, the neighbor residues connect to the loops will also move. I tried to fix the native structure with -loops:fix_natsc, and also try to set the neighbor distant to 0, but all failed.

The command was:

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How to import SymmDock models into Rosetta for local docking and energy minimization

We are dealing with a gap-junction protein which forms a hexamer of identical subunits. Now, we want to dock the subunits into a hexamer to examine the overall complex structure. Initially we have created models of docked complexes of our protein on the Symmdock server. Now we want to import the Symmdock models into RosettaDock server for a local docking search. Please help rearding how to import SymmDock models into Rosetta for local docking search and energy minimization

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Over-docking with FlexPepDock

I'm docking a short peptide fragment (2 residues) into a small binding pocket that only accommodates one residue. Since the binding pocket is hydrophobic and binds hydrophobic peptides, I expected that Rosetta would give a poor score to peptide mutant such as lys, his, arg. But it scores these quite well. If I don't dock, but just score after using the fixed backbone protocol to make the mutants, the results are quite good. However, sometimes there is a lot of clashing, and the peptide's side chain is pointed out of the binding pocket.

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protein protein docking pipeline

After going through the tutorials of protein protein docking, I totally got in a mess.
The flag file and XML file, low resolution and hign resolution docking, clustering seem to mix together.
1. $docking_protocol.linuxgccrelease -database $ROSETTA_DATABASE @flag > log.txt
The flag file as follows:
-parser:protocol low_res_docking.xml
-s input.pdb
-dock_pert 8 5
-spin 1
-docking_centroid_outer_cycles 50
-docking_centroid_inner_cycles 500
-docking:dock_mcm_trans_magnitude .1
-docking:dock_mcm_rot_magnitude 1
-nstruct 10
-linmem_ig 10

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Loop Modelling: ERROR: switch_to_residue_type_set fails

I tried adding the patch files pro_hydroxylated_case21.txt and pro_hydroxylated_case2.txt to
../rosetta_database/chemical/residue_type_sets/centroid directory and also adding the file names to the patches.txt file.

I still get the above error.

Example of patch file:

NAME pro_hydroxylated_case2

## general requirements for this patch


## now we search for a case that matches the residue, take the first one
## so put generic case last

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Error when renumbering PDB

Hi,I am a new Rosetta learner, just following the protein protein docking tutorials to study now.
In the protein preparation step, an error turned up as follows:
$ python ~/rosetta_scripts/scripts/ complex.pdb ignorechain
Looking for: complex.pdb
Found preoptimised or otherwise fixed PDB file.
Traceback (most recent call last):
File "/home_soft/home/simm05/rosetta_scripts/scripts/", line 156, in ?
if (chainid == line[21] or ignorechain or removechain):
IndexError: string index out of range

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