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Loop modeling/closure for many structures

Submitted by sn on Mon, 2017-03-06 11:25
Category: 
Loop Modeling

Hi,

I am trying to do homology modeling. I thread around a thousand structures. Before performing the energy minimization, I want to identify broken structures and  stitch them. What are the possible ways to do it? So basically,

1. I want to identify those structures that require loop modeling (broken structures)

2. Perform loop modeling on all those (say there are a couple of hundred structures).

3. Then perform energy minimization.

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Rosetta 3 - Applications

combine_silent ERROR: unknown atom_name: CYS SG

Submitted by freedman on Mon, 2017-03-06 10:56
Category: 
Structure prediction

Dear Rosetta experts,

I am trying to combine some silent file representing proteins that have disulfide bonds (combine_silent.linuxgccrelease from rosetta/2015.25.57927).  The silent files were created by running minirosetta for structure determination.  I am running into the following error message:

[ERROR] EXCN_utility_exit has been thrown from: src/core/chemical/ResidueType.cc line: 2975
ERROR: unknown atom_name: CYS  SG

Can anyone please tell me how to get around this error?

Thanks,

Holly Freedman

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Rosetta 3 - General

Building a PDB from a set of internal coordinates.

Submitted by jcminerlanl on Mon, 2017-03-06 09:47
Category: 
Structure prediction

I am curious if anyone knows of a program in Rosetta that can build a protein or non-canonical polymer chain based on a set of internal coordinates and other geometric criteria?

Specifically I want to find a program that can take a set of dihedral angle data (with the possibility of including long-range, inter-residue contacts) and use these data to generate the Cartesian coordinates of the molecules.

If anyone knows of a particular program in Rosetta that can accomplish this, please point the way.

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Rosetta++ - General

Looking for collaboration.

Submitted by ac.research on Mon, 2017-03-06 04:54
Category: 
Design

​Dear Rosetta Community,

 
I am searching for labs in the UK that uses rosetta to design proteins for collaboration. Is there a list of all labs that either develop or use rosetta?
 
Why the UK? becuse the funding I will bring will be from a UK based institute.
 
Just a list, or where I can find one, will be helpful enough.
 
Thank you.
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Rosetta 3 - General

Perform MPI relax with movemap files

Submitted by sn on Sun, 2017-03-05 13:18
Category: 
Constraints

Hi,

I want to relax around 3K structures. Also, I have a movemap file for each of these structures. How do I trigger mpi runs for relax with movemap files?

Earlier, when I did not need the movemaps, I used the following command:

mpiexec -np 32 $ROSETTA/bin/relax.mpi.macosclangrelease -in:file:l <pdb list file> -nstruct 20

But, now I want to perform relax with move map associated with each of the pdb file in the pdb list file. How do I do it?

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Rosetta 3 - Applications

[dev] not seeing energy in pose row for new energy term in design

Submitted by ipetrik_ambry on Fri, 2017-03-03 13:16
Category: 
Scoring

Hi all,

I made an EnergyMethod to add a few new energy terms and am trying to use them in fixbb. However, for two of these terms, the 'pose' row shows only 0, even though the individual position rows show non-zero values that sum to non-zero. This is how I set my terms in the emap:

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Rosetta 3 - General

Error of non standard amino acid (SnugDock)

Submitted by bt13d072 on Wed, 2017-03-01 19:51
Category: 
Docking

Hi

I am trying to do a docking with an antibody molecule and its partner protein. As far as I can see, the amino acid residues are perfectly fine. Yet when I try submitting it, I am getting an error about non-standard AA. Please find attached the screenshot of the error message.
Kindly help me get through this problem.

Thanks

Suchetana

 

I am also attaching the input file (though this is not the complete file. I am unable to upload the complete file for size issues. Please suggest a workaround)

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ROSIE - General

[dev] Using h-bonding values in new energy term

Submitted by ipetrik_ambry on Wed, 2017-03-01 11:33
Category: 
Scoring

Hi all,

I'm implementing a new energy term and need to weight it based on the bb h-bonding energy of this residue and the two residues it is bonded to. It is a ContextDependentOneBodyEnergy and I have everything working except this weight. Obviously rosetta already has methods that calculate hbond_lr_bb and hbond_sr_bb. My question is - what is the best way to get the hbond energys of the residues in my energy method?

Thanks!

-Igor

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Rosetta 3 - General

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