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Please help - mpiCC Error

Submitted by Prasanth Kumar on Wed, 2013-07-17 07:46

I'm trying to install mpi version of rosetta-3.4 in cluster.
I got the error when i did "scons bin mode=release extras=mpi (with and without cxx=icc) ", mpiCC : Command not found

In the cluster there is mpicc, mpicxx. There is NO mpic++, mpiCC.

What should i do now?

How do i install mpiCC without administrative previleges?

Please help me:)

Note:- I'm from non cs background.

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Rosetta 3 - Build/Install

select_best_unique_ligand_poses output

Submitted by ast on Thu, 2013-07-11 02:33

For select_best_unique_ligand_poses output: is there a way to show the number of poses that he did not wrote out because the rmsd is too near to an already outputted pose for each outputted pose seperately? That is, sort of the "cluster" size.
Thanks

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Rosetta 3 - Applications

Changing constraints code and compiling

Submitted by Ashafix on Sat, 2013-07-06 05:13

Dear Rosetta community,

after reading a lot of helpful posts I managed to compile Rosetta 3.4 on Ubuntu 11.04 in a virtual machine on Windows 7. It runs without any problems and abinitio folding actually works.
I wanted to add a new constraint function (just to test some weird idea, don't ask), unfortunately I neither speak C++, nor understand how the inner organs of Rosetta work.

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trouble in floppytail modelling

Submitted by ytao on Thu, 2013-06-27 13:15

Hi,

I'm using floppytail app (rosetta 3.5) to model my protein complex. The first chain in pdb file is a 353 residue protein and the second chain is a 138 residue protein. The "floppytail" region is N-terminal residues 1-37 in the second chain.

In the generated structures I noticed that the N-term residue of second chain (beginning of "floppytail") is not moving in space. All generated structures overlap in first chain(residue 1-353), and the first residue of second chain(residue 354 in pdb). I think the first chain is not supposed to move but I wanted N-term of second chain to move.

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Rosetta 3 - Applications

missing amino acid

Submitted by berk on Fri, 2013-06-14 06:07

I have a crystal structure that has 3 missing amino acid in its loop site,
How can I add the missing amino acid to the structure to remodel it.

Thanks,

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Rosetta 3 - General

strange effect in: SymDock.linuxgccrelease

Submitted by ast on Tue, 2013-06-11 11:05

Hi,

I have a strange problem regarding SymDock:
I did symmetry Rosetta previously using RosettaScrips 3.4. And it worked fine so far. Since I want to do docking on that symmetric molecule and - at least to my understanding - the Docking is not ported to Scripts for symmetry mode, I choose to use SymDock.
When I try to run it with exactly the same .pdb .sym and .params as in Scrips (which worked fine!) I get "
"...
protocols.simple_moves_symmetry.SymDockingInitialPerturbation: initialize_rigid_body_dofs: true

ERROR: unrecognized atom_type_name COO

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Rosetta 3 - Applications

Loop modelling,

Submitted by berk on Sat, 2013-06-08 08:29

Hi,

I preform using loop modelling base of fragment database to remodel the loops of a protein,
But when it generates several models (e.g., 10000), it changes the other part of the protein (e.g., helix conformer) too.
But I expect , only remodels the loops site not other sites.

Thanks

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