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How to automatically position new peptides into the binding site of a enzime, in order to run peptide-protein docking approaches

Submitted by zaldini on Fri, 2015-01-02 05:53
Category: 
Docking

Hello,
I would like to know how to automatically position new peptides into the binding site of a enzime, in order to run peptide-protein docking approaches?
In my case, I know the binding site and I have the crystallographic structure of a reference peptide located at the binding site, but I need to generate several (thousands) of other new linear peptide structures at this same binding site, in order to run the docking calculations using the rosetta3 protocols.

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Rosetta 3 - General

Docking with constraint

Submitted by Hongtham on Sat, 2014-12-27 09:56
Category: 
Docking

Hi everyone,
I am trying to dock a domain into a dimer protein. The domain is lowest score structure that was generated by abinition relax. Because they are continous amino acid sequence, so i use atompair constraint betwen c terminal of first monomer with n terminal of predicted domain. I also constraint its c terminal with n terminal of the second mononer.

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Rosetta 3 - Applications

Different scoring applications (score vs score_aln vs score_jd2, etc.)?

Submitted by cossio on Fri, 2014-12-26 07:19
Category: 
Scoring

What's the difference between the different scoring applications?

In my bin folder I find the following scoring applications:

score, score_aln, score_aln2, score_jd2.

What's the difference between them?

(I am omitting the trailing .default.linuxgccrelease, or mpi.linuxgccrelease, since I know those denote parallel vs non-parallel versions)

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Rosetta 3 - Applications

score application

Submitted by Hongtham on Tue, 2014-12-23 06:38
Category: 
Structure prediction

Hi everyone,
I want to ask a question.
I have some protein structure and i want to calculate their score and chose the one which has lowest score. I used "score_jd2.mpi.linuxgccrelease" to get score.
But the output file pdb has different Hydrogen coordinate even I used the command "no_optH true" to keep the Hydrogen atom position.
I dont understand why it happened.
and which structure should I use for following job? the inital structure of the output pdb after running score command?
Thank you so much.
Hongtham

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Rosetta 3 - Applications

why energy is positive?

Submitted by albumns on Tue, 2014-12-23 00:05
Category: 
Loop Modeling

Hello:

I am using kic loop protocol to refine a big loop with 12 aa with rosetta. I noticed that the energy is positive from generated .PDB file:

#END_POSE_ENERGIES_TABLE ./my_0002.pdb
chainbreak 0.00388937
loop_cenrms 0
loop_rms 0
total_energy 189.805

Shouldn't it be a negative value in principle?

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Rosetta 3 - General

Combine flags file with command line arguments?

Submitted by cossio on Mon, 2014-12-22 13:52
Category: 
Compilation
Structure prediction
Docking
Design
Scoring
Enzyme Design
Loop Modeling
Constraints
Symmetry
Small Molecules
Chemically Modified Residues
Fragment Generation
Membrane
Non-Canonical Peptides
Nucleic Acids
Phenix / MR Rosetta

Is it possible to combine a flags file with command line arguments?

For example, something like this:

minimize_with_cst.linuxgccrelease -in:file:l min_pdb_file_list @flags_file

where flags_file contains additional options. Moreover, what is the effect of changing the order of command line arguments and flags files? Which takes precedence? That is, what is the difference between the above command and:

minimize_with_cst.linuxgccrelease @flags_file -in:file:l min_pdb_file_list

Thanks.

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Rosetta 3 - General

About missing disulfide partners for residue...

Submitted by Mon on Wed, 2014-12-17 05:37
Category: 
Loop Modeling

Dear experts,

I'm trying to evaluate the energy of a 12 residues loop (residues 48-59) without considerint its environment. This loop contains one disulfide bond between residues 48 and 111. Since this bond links one loop CYS with another CYS located outside, when I trim the loop (dummy) from the full structure (pose) with grafting functions:
rosetta.protocols.grafting.delete_region(dummy,60,pose.total_residue())
rosetta.protocols.grafting.delete_region(dummy,1,47)

and I evaluate energy:
scorefxn(dummy)

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PyRosetta - General

Error MPI build rosetta2014.35 on Ubuntu14.04 LTS

Submitted by syoifczeri on Tue, 2014-12-16 02:35
Category: 
Compilation

Hello!

Recently, I posted some post about install Rosetta3.5 on cygwin.

Finally, I changed the OS and succeeded to install them on the Ubuntu on Virtual box(Win7)
Normal install was good. and docking protocol was worked(I only checked that exe).
./scons.py -j4 mode=release bin

But,I couldn't MPI install by follow command in another new Virtual machine. The first one hour from the beginning was good but I got some error.
I did all command as superuser

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Rosetta 3 - Build/Install

Segmentation fault

Submitted by Hongtham on Mon, 2014-12-15 20:21
Category: 
Structure prediction

Hi everyone,
I tried to run protocol AbinitioRelax to predict the structure of a sequence amino acid.
Howerver, I just could run this protocol with less than 11 cores (CPU processor). If I increased the core number more than 11, the protocol couldn't be run, even my PC has 12 or 16 processor. It returned the "Segmentation fault (11)" and cancel the job.
It doesn't happen the same problem when I run the protocol Flexpepdock.
Did anybody meeting the same problem with me?
Can anybody help me solve this problem?
Thank you so much.

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Rosetta 3 - General

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