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error during docking

Submitted by zhisheng on Thu, 2012-02-02 12:10

Hello,

When I start running docking calculation (docking_protocol.linuxgccrelease), there was an error:

ERROR: total_residue() != 0
ERROR:: Exit from: src/core/pose/Pose.cc line: 1290

The command I used (just for test)t is:

dock -in:file:s ./prepack_protein.pdb -in:path:database $database -docking:docking_local_refine 1 -docking:dock_pert 3 8 -docking:spin 1 -docking:dock_min 1 -docking:partners [A_B] -docking:sc_min 1 -nstruct 50 -ex1 -ex2 -out:path:pdb ./path/ -out:file:scorefile ./path/

What's the problem? Or the prepack pdb file?

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Rosetta 3 - General

Docking double-stranded DNA to a protein

Submitted by xpzhang on Tue, 2012-01-31 12:35

I wonder if there is an example or tutorial for DNA-protein docking. How to prepare the file? Which command and flags to use?

My dsDNA is about 20 bps, protein has about 600 Aa. I would like to find the DNA interaction surface on the protein.

Any suggestion for other software, or sharing your successful experience would be highly appreciated.

Thanks!

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Rosetta 3 - General

rosetta 3.3 installation error on ubuntu 11.10

Submitted by xtalqin on Sat, 2012-01-28 18:07

hi everyone;

Hard time installing rosetta on ubuntu 11.10.
different problems, very frustrating.

Linux 3.0
ubuntu 11.10
python 2.7
gcc 4.6

Here is the recent one；

/tmp/ccIDDP8t.s: Assembler messages:
/tmp/ccIDDP8t.s: Error: .size expression for _ZN7utility7options15VectorOption_T_INS0_19PathVectorOptionKeyENS_4file8PathNameEE5valueERKS4_ does not evaluate to a constant
/tmp/ccIDDP8t.s: Error: .size expression for _ZSt22__uninitialized_move_aIPN7utility7options10PathOptionES3_SaIS2_EET0_T_S6_S5_RT1_ does not evaluate to a constant

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Rosetta 3 - Build/Install

Altering Score/EMapVector

Submitted by mmertens on Fri, 2012-01-27 09:33

Hello,

I would like to alter the energies of some residues in a pose after applying the scoring function. I want to do something along the lines:

pose.energies().residue_total_energies('some resi')[fa_atr] = 'some value'

Obviously this is not directly possible, since:

"TypeError: 'EMapVector' object does not support item assignment"

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PyRosetta - General

loopmodel issue

Submitted by chiendarret on Fri, 2012-01-27 00:51

I am trying to use loopmodel to fold a linear peptide of 216 standard aa (obtained from the only existing data: fasta file, by using either the BuildPeptide or FragmentPicker executables of rosetta3.3).

I first tried "loopmodel.mpi.linuxgccrelease" (in my Open MPI compilation :scons bin mode=release cxx=gcc cxx_ver=4.6" ALL executables are both ".mpi." and non-mpi, which is strange as not all are parallelized) according to the command line:

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Rosetta 3 - Applications

Rosetta3.3 enzyme_design errors

Submitted by jtmacd on Wed, 2012-01-25 03:33

Hi all,
Has anyone else experience stability issues with the enzyme_design app compiled with the Intel compilers? I am getting bus errors/seg faults sometimes, but not when I run exactly the same input with a binary binary compiled with GCC.

As a separate I am also coming across this error sometimes:

ERROR: Dispatch error. Arrived at TrieCountPairGeneric with incompatible count pair data!
ERROR:: Exit from: src/core/scoring/etable/etrie/TrieCountPairGeneric.cc line: 473

Has anyone come across this error?

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Rosetta 3 - General

rmsd and Lrmsd in loop modeling

Submitted by Victor on Tue, 2012-01-24 09:52

Hi,

I have a question about output file test_loop_output.fasc in
an example of Cyclic Coordinate Descent loop closure - loop_modeling.py.
Here we have rmsd and Lrmsd, what is the difference?
In manual you can find that Lrmsd is the rmsd of all loops in the reference
frame of the fixed protein structure.
What does it means? What is rmsd?
How to find rmsd for all loop backbone atoms?

Thank you,

Victor

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PyRosetta - General

dun10

Submitted by jadolfbr on Thu, 2012-01-19 12:16

Hi,

Just curious if there is or there will be a flag to use Roland's 2010 Rotamer library within Rosetta. We have been replacing the 2008 binaries with data using the 2010 library and then using the 2008 flag, which works well enough. I'm still learning C++, or I would try and implement it myself.

Also, if it does already work within Rosetta, where would I find it within the code, and which level of smoothing was used? (optim, 5%, 20%)? We have been using optim (with the neighbor-dependent ramachandran flag) across most of Rosetta's apps and it seems to work well.

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Rosetta 3 - General

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