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protein protein docking pipeline

Submitted by dzhao on Thu, 2012-07-19 06:25

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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Rosetta 3 - General

Loop Modelling: ERROR: switch_to_residue_type_set fails

Submitted by smiruthi on Wed, 2012-07-18 14:48

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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Rosetta 3 - General

Error when renumbering PDB

Submitted by dzhao on Wed, 2012-07-18 01:03

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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Rosetta 3 - General

how to score a pdb in rosetta 2.3

Submitted by Lindsay on Tue, 2012-07-17 08:42

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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Rosetta++ - General

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

Submitted by Lindsay on Mon, 2012-07-16 13:12

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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Rosetta++ - General

unknown constraint function type: AtomPair ?

Submitted by jiongzhang on Sun, 2012-07-15 02:13

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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Rosetta 3 - General

optH flag makes hydrogen bond energy scores worse...

Submitted by tsjain on Fri, 2012-07-13 14:04

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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Rosetta 3 - General

Output different favored solutions with PackRotamersMover design

Submitted by xfliu on Fri, 2012-07-13 06:23

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]

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PyRosetta - General

Rosetta 3.3 installation in linux

Submitted by Ramya on Thu, 2012-07-12 13:55

Hi,

I 'm experiencing an error with Rosetta 3.3 installation in CentOS (free OS of Red hat Enterprise) virtual machine. Its version is 5.8 for a 32bit windows machine. Once i successfully installed scons, i ran this command
"scons bin mode=release" to install rosetta with root permissions in my virtual machine. After a 2 hour compilation, it gave an error saying that it couldn't find "lz" file in my root directory. Below is the error message. Any help on this is appreciated.

/usr/bin/ld: cannot find -lz
collect2: ld returned 1 exit status

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Rosetta 3 - Build/Install

Docking structures with ligands in cryo-EM maps

Submitted by galushin on Wed, 2012-07-11 12:40

Greetings Rosetta gurus-

We are attempting to use Rosetta 3.3 to flexibly dock crystal structures into relatively high resolution (around 4.8 Angstroms) cryo-EM maps. Our protein of interest binds and hydrolyzes GTP, and oligomerizes in a nucleotide-dependent manner. We have cryo-EM structures of the protein in GDP and GTP states (bound to a non-hydrolyzable analog) in physiological oligomers, and crystal structures of the protein in both nucleotide states in non-physiological conformations/oligomerization states.

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Rosetta 3 - Applications

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