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RosettaMatch outputs

Submitted by mwfranklin on Tue, 2016-10-11 11:46
Category: 
Design
Enzyme Design

I've been running several rounds of RosettaMatch lately and I'd like them to go faster. I'm pretty sure writing matches is the part slowing it down. Is there anyway to limit the number of matches it outputs? For example, for the same matched sequence (say H133H135H432), I get anywhere from 50-400 cloudPDB files. I don't want more than the first one or two, because the rest are almost always just different ligand positions and I'll end up running EnzDesign anyways. I'm using these flags:

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Rosetta 3 - Applications

mpi installation issues

Submitted by banshee on Tue, 2016-10-04 18:48
Category: 
Compilation

hi all

i am trying to build mpi version of rosetta 3.7 on a machine with redhat linux (I have no problem installing on Ubuntu). I copied the topsail site.settings file and commented out the path to INCLUDE because initially rosetta complained about no INCLUDE parameter.

I compile by using scons(scons -j8 bin mode=release extras=mpi) and the compiling ends fine, no error, no stalling, but when i execute the executables (for instance fixbb) i get the  message below:

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Rosetta 3 - Build/Install

How to transform a pose from symmetric into non-symmetric?

Submitted by msardejani on Tue, 2016-10-04 16:55
Category: 
Design
Scoring
Constraints
Symmetry

Hello,

Is there a way to break the symmtery of a pose in the middle of a Rosetta script? I want to avoid writing the PDBs and feeding them again to a new script.

Any suggestion is highly appreciated!

Thanks!

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Rosetta 3 - General

symmetric design in the presence of a nonsymmetric ligand

Submitted by msardejani on Fri, 2016-09-30 15:17
Category: 
Design
Symmetry
Small Molecules

Hello,

I am trying to design a C3 symmetrical protein with a ligand bound at the C3 interface. What is the best way around this in RosettaScripts? I was thinking to first symmetrize the pose with SetupForSymmetry and then add the ligand with AddChain mover. But it seams, SetupForSymmetry is not compatible with extra_res. As soon as the script arrives at SetupForSymmetry, it throws the following error:

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Rosetta 3 - Applications

Histidine protonation

Submitted by DmitriiN on Mon, 2016-09-26 13:15
Category: 
Chemically Modified Residues

Hello, everyone!

I have histidines in my protein and they seem not to have not a usual "HIS" protonation state. I think it is in "HSD" state, but this seems to be noncanonical. I found the HIS_P.params somewhere in the database, but it doesn't seem to work.

What should I do?

Dmitrii

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Rosetta 3 - General

DomainAssembly Mover with constraints (using RosettaScripts)

Submitted by resiros on Wed, 2016-09-21 11:19
Category: 
Docking
Scoring
Constraints

Hello,

I am trying to run the domain assembly protocol while atom_pair constraints . I am using RosettaScripts for my application.

I have tried including the constraint file in the xml script using the ConstraintSetMover and Reweighting the score function. I have also tried included the constraint file in the flag file using -constraint:cst_fname. Yet the output silent do not seem to include the atom_constraints score term.

I would appreciate any help on how to include the constraints in the scoring function for domain assembly.

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Rosetta 3 - General

Rosetta remodel on intel Xeon Phi

Submitted by pablogalazdavison on Wed, 2016-09-14 15:35
Category: 
Compilation

Greetings, I am planning to use Rosetta Remodel very soon, and as I am designing a system to do so, I found myself wondering if I could use the xeon phi coprocessor's cores to increase output. I believe it can be done with mpi, but I am uncertain about that, performance and how difficult the setup would be.
Also, about how many RAM is required per core? I remember that certain steps in remodel protocol require quite an amount of RAM, and the Xeon Phi I am trying to get hands on is 8GB for 60 cores.
Any insights is really appreciated.

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Rosetta 3 - General

rosettaCM not recognizing Mn atom

Submitted by banshee on Mon, 2016-09-12 23:33
Category: 
Structure prediction

hi i am running rosettaCM with a protein which has a ligand and a heavy atome molecule, MN.

I input a params file for the ligand which rosetta sees ok, but it gives an error saying that MN is unrecognized residue.

I confirmed that MN.params file is in the right directory and the the txt file which specifies residues has the MN in it.

I also tried to input the MN.params file directly using -extra_res_fa flag but the error remains.

is metal ions not allowed when running rosettaCM? thanks.

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Rosetta 3 - Applications

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