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add water into protein interfaces using solvated rotamer?

Submitted by chinhsutran on Sat, 2013-07-20 07:33

Hello,

Im new to Rosetta. Im trying the tutorials of PyRosetta, but I couldn't find any clues that could help me add water into the protein interfaces using the Solvated Rotamers (as stated in the paper by Jiang et al. 2005 "A solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces).

Anyone please suggests me any hint or readings that I can find how to do it!

Thank you very much.

Regards,
Chinsu

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PyRosetta - Scripts

A problem with RosettaLigand

Submitted by Rosettasz on Fri, 2013-07-19 16:09

Hello, everyone,

I just started to learn Rosetta, and was wondering if I could get some help here.

I was trying to follow the Ligand Docking example which was used during the Workshop held in April this year .
While the protocol was done with rosetta3.5, I am using rosetta3.4.
And I got some problems during the run.

I prepared the following files as instructed:

receptor: 2Q5K_mutant.PDB
Ligand: SAQ_aligned.pdb
Ligand conformers: SAQ_conformers.pdb
Ligand parameter file: SAQ.params
Water: water.pdb
XML file: water_dock.xml
option file: options.txt

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Rosetta 3 - Applications

Loop prediction

Submitted by yzhou on Thu, 2013-07-18 14:24

A protein is composed of N and C domains.
In the experiment, the protein was cut into these two domains and each of them was solved by crystallography.
However, the structure of the loop linking these two domains was unknown.
Therefore, I hope to predict the loop structure so that it can link the solved two domains.
How to achieve this goal?
Look forward to the reply.
Thanks.

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Rosetta 3 - Applications

Unsatisfied interface H-bond in Ligand docking

Submitted by Prasanth Kumar on Thu, 2013-07-18 12:04

I am leaning docking with 3dau. I followed the documentation: I went to docking after repacking the cofactor using ligand_rpkimin and then appended the ligand cofactors.

~/rosetta-3.4/rosetta_source/bin/ligand_dock.linuxgccrelease -database ~/rosetta-3.4/rosetta_database/ -s 3dau_aligned_plus_nap_plus_mtx.pdb -in:file:extra_res_fa ~/Desktop/docking_3DAU/NAP.params ~/Desktop/docking_3DAU/MTX.params -ex1 -ex2 -ex1aro -nstruct 1 > out.log

I got something interesting in the log; But there were NO errors or warning:-

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Rosetta 3 - Applications

high-res docking

Submitted by tfliu on Mon, 2013-07-15 02:49

Category:
Docking
Hello:
After low-res docking,I'm going to do high-res protein/protein docking.There are two modes(High Resolution Docking Only;High Resolution Docking minimization)in the rosetta3.4 user guide.Which one should I choose?
Here is my flags:
1.High-res docking only flags
-s 1.pdb

-partners ABC_DE

-ex1

-ex2aro

-use_input_sc

-docking_local_refine

-nstruct 1000

-mute core.util.prof

-out:overwrite

-out:pdb

-mute core.io.database

2.High-res docking minimization flags
-s 1.pdb

-partners ABC_DE

-ex1

-ex2aro

-use_input_sc

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Rosetta 3 - Applications

Clustering using an disrupted run silent file

Submitted by PaulaBanks on Mon, 2013-07-15 02:19

Hi all,

I was running rosetta but something happened and the job was stopped. I would like to use the already generated silent file to cluster but when I run the clustering algorithm I get a 'could not make' error which I suppose is due to the incomplete status. Had set to generate 10,000 but at the point of interruption there were 4767 structures. How do I edit the silent file for proper clustering of the 4767 decoys?

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Rosetta 3 - General

Unrecognized aa NO3

Submitted by JadAbbass on Sun, 2013-07-14 10:48

Dear all,

I am trying to predict the structure of 2XSE using "Abinitio", the following message appeared:

-------------------------------------------------------------
ERROR: unrecognized aa NO3
ERROR:: Exit from: src/core/io/pdb/file_data.cc line: 972
--------------------------------------------------------------

According to the pdb file, it is an ion (preceded bu HETATM).

1- How to create a new parameter file for the residue?

2 - Can I simply remove those lines form the pdb file? Will the prediction process continue normally?

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Rosetta 3 - General

Ligand conformations file in docking

Submitted by rosa on Fri, 2013-07-12 09:21

All,

I have a multi-ligand file, NBU_confs.pdb, of ligand conformers (291 total) and the line "PDB_ROTAMERS NBU_confs.pdb" at the end of the params file, and the pdb (coordinates) of one of the ligand conformers at the end of the input receptor file for docking. My questions:

1. Does Rosetta use the other conformers in NBU_confs.pdb. If so why does it need to have the pdb of just one conformer at the
end of the input receptor file?
2. If I run on several CPUs, each with -nstruct 1000, using the same input receptor file, params, options etc..., would the

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Rosetta 3 - General

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