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RosettaAntibody

I have been using Rosetta for about a year now and have been interested in using RosettaAntibody for some time now. I have held off installing Rosetta++ in the hopes that RosettaAntibody would be included in the new 3.2 build. Does anyone know if this is the case, or will I still need to install Rosetta++ in order to access that algorithm without taking up space on the RosettaAntibody webserver?

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loop model error

Dear:
I am trying to run the loop model protocol by the command: loopmodel.linuxgccrelease @kic.options

However, it doesn't work, and here is my log file. I would be very appreciated if you can give me some advices.

By the way, does the loop protocol support MPI?

Thank you very much

-------------------------------log-----------------------------------------------
core.init: Mini-Rosetta version exported from unknown
core.init: command: loopmodel.linuxgccrelease @kic.options

Post Situation: 

How do I add hydrogen atoms to my PDB file?

I'm currently using Rosetta 3.2.1, and I wish to add missing H atoms to my PDB file. I know that in the past, a clean_pdb.py script was created by the Meiler Lab to help with such a problem. However, I'm unable to locate this file anywhere in Rosetta 3.2.1. Is there any ways to locate this file or is there other scripts made to satisfy such a problem.?

Thanks.

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Why a paralleled Rosetta perform like a normal one?

Hi all,

I newly built a paralleled Rosetta2.3.0 with OpenMPI 1.4.3. I used "make mpilam" to build it.
After building, I tested it with the following command:

mpirun -np 16 /home/knight/softwares/Rosetta-2.3.0/rosetta++/bin/rosetta.mpilam -mpi_task_distribution -s 1ubq.pdb -design -fixbb -resfile resfile -ex1 -pdbout test -ndruns 2000 > 1ubq_fixbb_mine.log

-np = 16 since I have 16 cores.

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Help with get_pdb.py for PDB file cleaning

Hi, I am following the suggestion from one of the posts here to use get_pdb.py to clean up my PDB files. However, I always got the error message:

Traceback (most recent call last):
File "/usr/local/rosetta3.2/rosetta_source/src/python/apps/public/get_pdb.py", line 69, in ?
assert( len(argv)>2)
AssertionError

Did I do something incorrectly? Thanks in advance for any kind help!

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help with perturbation docking please

We ran a centroid blind docking for a published reference system. [Its docking had been calculated with BiGGER - don't know if this is relevant]. We ran 1000 structures. Among the 5 most negative scores was a structure that looked as if it could be perturbed into one that resembles the structure in the literature. We ran full atom perturbation docking with an angle of 45 deg & a 10A distance.

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abintio clustering - funnel plot

Hi,

i have run abintio structure prediction and produced nearly 20.000 structure. please help me how to cluster these structures and how to create funnel plot to select native like structure from silent file. Do u think 20,000 structures is good enough to predict native struture of 146 residues. Is there any way to filter strutures using secondary structure prediction during clustering stage. I know rosetta 3.2 supporting SS based filtering but i have all my predictions with rosetta 3.1.

Thank you in advance for all your help

with regards,
vamsi

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