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Garbled Ligands from docking_protocol

Submitted by skovacs on Tue, 2011-12-20 07:55

Greetings,

I'm trying to construct a homo-dimer of a protein+ligand (so a total of two peptide chains and two ligand chains) using docking_protocol with the -docking::partners flag.
I've parameterized the ligand using molfile_to_params.py and docking_protocol runs without generating any fatal errors (although there are numerous warnings about discarding atoms, missing heavyatoms, can't find atoms, etc.).
However, when I check the output structures, I find that both peptide chains are intact but both ligands have completely come apart.

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Rosetta 3 - Applications

Rosetta ab initio with disordered regions

Submitted by smiruthi on Thu, 2011-12-15 14:37

I don't have experimental data on the disordered region of a protein and tried different online prediction servers and obtained contradictory results. Disopred2 was used in the Wang et al PLoS 2011 rosetta paper but I am not sure about the accuracy. I was wondering if there were any suggestions on how to proceed?

Thanks a priori.

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Rosetta 3 - General

ERROR: unrecognized residue name 'GLY_p:RepulsiveOnly'

Submitted by smiruthi on Mon, 2011-12-12 14:27

I get this error when I try to combine my silent files (using Wang et al Disorder predictions with REPLONLY residues:

core.io.silent: Finished reading 2744 structures from silent_1270984.mgt.out

ERROR: unrecognized residue name 'GLY_p:RepulsiveOnly'
ERROR:: Exit from: src/core/chemical/ResidueTypeSet.hh line: 151

Thanks a lot a priori.

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Rosetta 3 - Applications

No read_resfile routine?

Submitted by gjbartlett on Mon, 2011-11-28 08:45

Hello,

I've been trying to run the Packing and Design tutorial with a view to writing my own Packing/Design routine. I'm following the pdf posted on the PyRosetta website and the errata page. There doesn't appear to be a read_resfile routine for either standard_packer_task (as per the original instructions) or create_packer_task (listed in the errata).

I get "AttributeError: 'PackerTask_' object has no attribute 'read_resfile'"

I'm running the latest Windows native build PyRosetta build. Any help gratefully appreciated.

Many thanks,

Gail

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PyRosetta - Scripts

limit_cluster_size default value

Submitted by sacch on Thu, 2011-11-24 17:57

Dear all,

I looked into the source code of Rosetta and found out that if in the input we don't assign -cluster:limit_cluster_size (default is -1), it seems the cluster size will be zero (line487~499, protocol/cluster/cluster.cc)? Could someone please explain what is going on here?

in line 495, there is screening of j<=limit, which means, if limit is negative, the cluster list will never be populated. The weird part is that I still get good clusters if I don't give this value in the input.

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