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how to generate Fragments using up to 2001 structures only

Submitted by oppopomoz on Sat, 2015-07-25 00:43
Category: 
Fragment Generation

Hello!

I am trying to replicate an old experiment and I'd need to generate fragments using old structures only. How can I do that?
at the moment I created a database of old structures and I downloaded the rosetta fragment picker tool so I am trying to find out what internal database of rosetta I should update, any suggestions?

Thanks a lot in advance

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Rosetta 3 - Applications

How to judge docking success for two proteins without knowledge of native structure

Submitted by jasnyderjr on Fri, 2015-07-10 14:27
Category: 
Docking

If you are trying to dock two proteins, using a global search, with no knowledge of correct answer (native structure) , how does one judge a docking success?. When reporting benchmark results, for example, the native (or mock-native) structure is used to rmsd against, and the definition of docking funnel is based on I_rmsd, so judgement of docking success is always based on some known (native) structure (or correct answer). Starting with just two proteins arbitrarily place apart.

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Rosetta 3 - General

molfile_to_params script error

Submitted by pablogalazdavison on Tue, 2015-07-07 21:22
Category: 
Chemically Modified Residues

Greetings, I've been following the "design with non-canonical aa" demo (located on demos/public/design_with_ncaa) in order to set parameters for a custom residue "CYM", which is a deprotonated cysteine. Yet I got stuck in the last step namely, when I try to convert my modified .mol file to params using:

"python molfile_to_params_polymer.py cym.mol --clobber --polymer --no-pdb --name CYM -k cym.kin"

it returns:

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Rosetta 3 - Applications

Cancel / delete Rosie not working

Submitted by fglaser on Tue, 2015-07-07 01:14
Category: 
Docking

Hi,

I am trying to Delete / Cancel jobs on Rosie that I suspect will fail, so I want to save running time and send another job.

But when I click on the Delete / Cancel links on my account fglaser_rosie, nothing happens....

What I am doing wrong?

Best regards,

Fabian
Technion, Haifa
Israel

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ROSIE - General

Job 「№15623」has failed

Submitted by fglaser on Tue, 2015-07-07 00:17
Category: 
Docking

Hi

Iam a newby with Rosie, I sent a PDB and sdf file with many molecules for Rosie docking, and I got the following input error message:

Job 「№15623」has failed with the message:

molfile_to_params step failed, please double check your input files!

I searched the documentation and for what I know the input PDB and the SDF where in correct format, but of course I maybe wrong...

Could you please explain me what exactly is wrong with the input and how to correct it?

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ROSIE - General

all warnings being treated as errors

Submitted by lah435 on Fri, 2015-07-03 15:31
Category: 
Compilation

My Rosetta build fails with: "scons: building terminated because of errors." However the errors really only appear to be warnings: "cc1plus: all warnings being treated as errors" (see below) How can I get scons to treat warnings as warnings and not as errors?

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Rosetta 3 - Build/Install

nbr_atom in ligand docking

Submitted by phanvy on Fri, 2015-07-03 07:40
Category: 
Docking

Dear all,
I run ligand docking protocol to dock a small chemical on my protein.
I set up the inital position of ligand is "-start_from 1.36 50.07 23.4".
Follow the document, the nbr_atom of the ligand is chosen near the inital position of ligand. But when I check the log file, I saw the nbr_atom of the ligand is far away from the inital position of ligand: 44.03500058226830 112.4592971897935 22.25074880071337
4.886590717968414 0.06526207982382815 17.92231676318689

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Rosetta 3 - General

When does Rosetta switch from centroid to FA mode?

Submitted by MarkW on Fri, 2015-07-03 04:48
Category: 
Structure prediction

HI,

I was wondering what criteria Rosetta uses to determine when it switches from centroid to full atom mode? Is it a set number of decoys, a target energy value, radius of gyration or something else?

Thanks

Mark

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Rosetta 3 - General

the output of ligand docking

Submitted by phanvy on Fri, 2015-07-03 01:27
Category: 
Docking

Dear all,
I run the ligand docking protocol to dock a small chemical to protein.
this is my flag
-packing
-no_optH
-ex1
-ex1aro
-ex2
-docking
-dock_pert 30 5
-ligand
-improve_orientation 1000
-minimize_ligand
-harmonic_torsions 10
-minimize_backbone
-harmonic_Calphas 0.3
-soft_rep
-old_estat
-start_from 1.36 50.07 23.4
-protocol abbrev2

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Rosetta 3 - General

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