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Version of VALL Database and Corresponding Constraint Coordinate File for Fragment Generation

Dear all,

I realized that the latest vall database that comes with Rosetta 3.2 is version 2006-05-05. Unfortunately, there is no corresponding constraint coordinate file ("vall_cst_coord.dat.") for that database. Both database files are only available for the 2001-02-02 version. Is there a way to get the constraint coordinate file also for vall 2006-05-05?
The 2001 version contains only one-third of entries in comparison to the 2006 version.

I want to use this for fragment picking using also my experimental NMR data (can't rely on Robetta).

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Problem with the -dock_ppk flag

Hey everyone,

I have been running protein docking with two monomeric proteins by using Rosetta3.2. Everything seemed to be fine with the docking runs except when I added the -dock_ppk line into the flags file.

Instead of having the -dock_ppk line in the flags file, I also tried to prepack the proteins by using the command line:

/usr/local/rosetta3.2/rosetta_source/bin/docking_protocol.linuxgccrelease -database /usr/local/rosetta3.2/rosetta_database/ -s input1.pdb -dock_ppk

It did not work either. Here is the last portion of the log file:

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Problem with symmetric docking

Hello everyone,
I'm trying to refine a homotrimer by using symmetric docking in Rosetta 3.2.1. I built the symmetry definition file and ran the following command:

~/rosetta_bin/docking_protocol.linuxgccdebug -database ../rosetta_database -in:file:s INPUT.pdb -in:file:fullatom -ex1 -ex2 -symmetry:symmetry_definition symdef.txt -symmetry:initialize_rigid_body_dofs -symmetry:perturb_rigid_body_dofs 3 8 -nstruct 1 -out:file:fullatom

Which yielded the following output

core.init: Mini-Rosetta version exported from unknown

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Symmetric docking - tetramer of trimers

I'd like to model a tetramer of trimers. In this situation I'm trying to ensure that all monomers end up on the same X-Y plane. Does anyone have any idea what my symmetry definition file should look like for this? Here's how I initially tried to do it, but I'm not getting reasonable looking structures:

------------------------------
symmetry_name sweeden_rules
subunits 12
recenter
number_of_interfaces 10

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test/run.py errors

When I input test/run.py on /resetta_source in rhel5.6 or 6,I all got the follow erros,
[root@localhost rosetta_source]# test/run.py -database /rosetta/rosetta_database
Identifying platform...

Platform found: debug/linux/2.6/64/x86/gcc/
Paths: cd build/test/debug/linux/2.6/64/x86/gcc/ && command line: ./protocols.test --database atabase
bash: ./protocols.test: No such file or directory
Paths: cd build/test/debug/linux/2.6/64/x86/gcc/ && command line: ./core.test --database atabase
bash: ./core.test: No such file or directory

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Using Rosetta Docking for nucleic acids

Hi,

I tried to use RosettaDock with protein-nucleic acid chains. But I have a problem. Rosetta doesn't seem to recognise nucleic acids with the parameters I used. Here is the error message:


ERROR: unrecognized aa U
ERROR:: Exit from: src/core/io/pdb/file_data.cc line: 534

The version of RosettaDock I compiled (3.2.1) worked with the protein-protein complexes I tried.

I suppose there is a command to specify nucleic acids or a specific database to use. Can anybody please tell me how to use RosettaDock for protein-nucleic acid chains?

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Will Rosetta Flexpepdock be adequate for this for now.?

Okie, if let's say I have the native structure of a protein-peptide complex, but I wish to only change 1 or 2 residues of the peptide, do you think it might still give me a relatively accurate result.? since I presume that there shouldn't be major changes to the secondary structure of the peptide.

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