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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

Post Situation: 

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.

Post Situation: 

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.
e.g.
1. $docking_protocol.linuxgccrelease -database $ROSETTA_DATABASE @flag > log.txt
The flag file as follows:
-parser:protocol low_res_docking.xml
-s input.pdb
-docking
-dock_pert 8 5
-spin 1
-randomize2
-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
-ex1
-ex2

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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
TYPES HYDROXYLATION

## general requirements for this patch

BEGIN_SELECTOR
PROPERTY PROTEIN
AA PRO
NOT VARIANT_TYPE HYDROXYLATION
END_SELECTOR

## 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/clean_pdb.py 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/clean_pdb.py", line 156, in ?
if (chainid == line[21] or ignorechain or removechain):
IndexError: string index out of range

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how to score a pdb in rosetta 2.3

Dear ALL,
I try to score a structure using rosetta2.3(with full atoms but don't need repack, just evaluate the structure). I found 4 ways to evaluate the structure in rosetta 2.3

0.1 score a structure without providing its native in fullatom mode

0.2 score a structure with providing its native in fullatom mode and repacking its sidechains

0.3 score a list of structure

0.4 score with termini residues

None of them can evaluate the full atom structure without packing. Is that any way for me to evaluation the structure? Thank you!

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Does rosetta 3.3 have different energy terms from 2.3 (fixbb design)

Dear ALL,
When I am looking the energy terms of the fixbb, I find that the rosetta 3.3 has terms as below
fa_atr 0.8
fa_rep 0.44
fa_sol 0.65
fa_intra_rep 0.004
fa_pair 0.49
fa_plane 0
fa_dun 0.56
ref 1
hbond_lr_bb 1.17
hbond_sr_bb 1.17
hbond_bb_sc 1.17
hbond_sc 1.1
p_aa_pp 0.64
dslf_ss_dst 0.5
dslf_cs_ang 2
dslf_ss_dih 5
dslf_ca_dih 5
pro_close 1.0

and
> hbond_sr_bb *= 0.5
> p_aa_pp *= 0.5
> rama = 0.2
> omega = 0.5

But 2.3 has only 11 terms.
bk_tot The total score using the design energy function. Lower is better.

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unknown constraint function type: AtomPair ?

Hi, when I tried to use constraints files with loopmodel, rosetta give the error message:

ERROR: FuncFactory: unknown constraint function type: AtomPair
ERROR:: Exit from: src/core/scoring/constraints/FuncFactory.cc line: 65

Could you help me to find out what's the problem?
Thank you very much!

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optH flag makes hydrogen bond energy scores worse...

I was trying to run rosetta.score with no_optH = false. However, when compared with the energies without hbond optimization, the hydrogen bond energies get worse, while the other components are unchanged. I have attached the input pdb file below.

Here are the command lines:
rosetta.score -database /usr/local/rosetta/3.3/rosetta_database/ -in:file:s test.pdb -out:output -no_optH true # Turn off hbond optimization
rosetta.score -database /usr/local/rosetta/3.3/rosetta_database/ -in:file:s test.pdb -out:output -no_optH false # Turn on hbond optimization

The output score file is:

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Output different favored solutions with PackRotamersMover design

Hi,

I'm trying to use PackRotamersMover to mutate a serials of mutatable residues into the predefined residues. Here is part of the core codes:

task = TaskFactory.create_packer_task(mutant_pose)
for i in range(1, mutant_pose.total_residue() + 1):
# only perform design for the mutatable residues
if i in mutation_positions:
# only mutate to specific amino acids types, like ["A", "K", "F", "S", "T", "K", "I"]
aa_allow = [False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False,False]

Post Situation: 

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