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Rosetta 3.3 installation warnings

Submitted by jjlee2 on Mon, 2011-11-21 09:19

I am trying to install Rosetta 3.3 on a cluster, but every time I try to install it, I get a ton of warnings (but no actual errors). I was wondering if these warnings are something I should worry about and, if so, how I should fix them. Some examples of the warnings are below and I have attached the whole error file.


src/protocols/toolbox/pose_metric_calculators/RotamerBoltzCalculator.cc: In mem\
ber function 'protocols::moves::MinMoverOP protocols::toolbox::pose_metric_calc\
ulators::RotamerBoltzCalculator::init_minmover(core::pose::Pose&, core::Size, b\

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Rosetta 3 - Build/Install

Hbond tripped

Submitted by alejandro on Mon, 2011-11-21 04:17

Good morning everybody,

I use Rosetta as part of a Monte Carlo algorithm. The main operations Rosetta performs are :
1) the scoring of a pose;
2) the modification of the pose (using modifications of the psi and phi angles, RigidBodyTransMovers and RigidBodySpinMovers).

It works quite well on average but sometimes, without any apparent reason, Rosetta crashes because of a "HBond tripped".

Can anybody help with that?

1) What does exactly this error mean?
2) Where does it come from (scoring functions or movers)?
3) Is it normal to get such an error ?
4) How do I get rid of it?

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Rosetta 3 - General

cluster.mpi running in MPI mode?

Submitted by sacch on Fri, 2011-11-18 23:30

Hi all,

I am aware that the application cluster does produce mpi version when rosetta is compiled in mpi mode. When I look into the output clog file in the folder, it seems all threads are doing identical procedures. I am wondering if it really used MPI to accelerate the calculation? Or is it just many threads doing the same job in the same time?

Thanks~

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Rosetta 3 - Applications

How to score the crystal structure?

Submitted by vsjasion on Fri, 2011-11-18 15:49

Hi All,

I have a control system in which the co-crystal structure is determined. I would like to have rosetta only score the input pdb without docking, so that I can compare the crystal coordinates with the results. I would also like to be able to score the prepacked structure used for the actual studies.

I used the flag -run:score_only and this worked, but there was a score.sc file and a pdb file. Also, the rms was 30 in the score file. I re-ran and sure enough, the score was different, indicating that it is actually docking not merely scoring.

The flags I used were:

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Rosetta 3 - General

loop modeling during enzyme design?

Submitted by lzx32 on Wed, 2011-11-16 00:30

Dear developers:

I noticed that some loop modeling options (e.g. kic_looop_sampling) are now included for the enzyme_design.linuxgccrelease protocol in Rosetta3.3.

It seems that the capacity to remodel loops in the substrate-binding pocket will significantly improve the enzyme_design protocol. But since this has not been mentioned in any papers or tutorials, are the loop modeling options fully working now, or are they still under development?

Thanks for reading...

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Rosetta 3 - Applications

fragment_picker with fasta only

Submitted by gw on Tue, 2011-11-15 13:20

I would like to generate a fragment library based on a sequence. I tried running the fragment_picker demos in rosetta3.3/rosetta_demos/fragment_picker and it seems I need to include a pdb and also psipred (.ss2) file. The documentation seems to say that only vall .fasta .wghts are mandatory. I only have sequence -- can I still run this protocol?
http://www.rosettacommons.org/manuals/archive/rosetta3.3_user_guide/app_...

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Rosetta 3 - Applications

ERROR: unrecognized atomtype property VIRTUAL

Submitted by harshkhare on Mon, 2011-11-14 09:40

Hello,
I have built Rosetta3.3 using gcc-4.3 which went smoothly without errors. While running any rosetta script(xml file) using rosetta_scripts.linuxgccrelease, i am getting the error 'unrecognized atomtype property VIRTUAL'. When the same script is run using rosetta_scripts.linuxgccdebug, the error doesn't occur. Please suggest me the solution for this error. Following is the error i am getting.
##BEGIN ERROR MSG##

protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job

ERROR: unrecognized atomtype property VIRTUAL
ERROR:: Exit from: src/core/chemical/AtomType.cc line: 108

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Rosetta 3 - General

Can not build the parallel version of rosetta-2.3.1 (the SnugDock). Help!!

Submitted by ice_flame on Fri, 2011-11-11 07:47

Hi all,

I was trying to build a parallel version of Rosetta-2.3.1(SnugDock) on my workstation. My OS is RHEL 5.4(32-bit), and I use Openmpi-1.4.3.

I tried to compile it as I did to Rosetta2.3.0 on the same computer and the very same OS and MPI compilier, but it didn't work.

I got the following errors:

######################
job_distributor.cc:(.text+0x5ada): undefined reference to `pathways::pathways_generator_main(bool&)'
collect2: ld return 1
make: *** [rosetta.mpilam] error 1

######################

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Rosetta++ - Build/Install

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