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Problems with the convergence of docking by the graph

I have been doing the docking with the program Rosetta
for an antigen-antibody complex
repeated runs and not get a graph
because the lowest energy structure
have a higher rmsd 5Ǻ
wanted to know if that's possible
really appreciate the attention you can give me.

attached a file with the results in pdf format

In these cases it will be worth re-do the docking from some of the results, ie, do a re-docking of the structure obtained in order to obtain a better convergence?

Post Situation: 

Memory Issues PyRosetta?

I´m running a Pyrosetta script on a 300aa protein with 30 mutable residues a packmover and a fastrelax (3 iterations each) on EX-level 4. When I allocate Memory below 16G I often have uncommented script abortions or "bad alloc" failures. Above 16G that never occurs. Now 16G is a lot and a lot more I seemed to need with Rosetta, albeit, not with the exact same job config. Is there a rule of thump concerning memory usage in PyRosetta? Comparisons with rosetta? Does anybody else encountered memory problems?

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fixbb design use

I read the manual of rosetta3.3, and found that there are at least 2 weights for fixbb design:
1. By default, the fixbb application uses the "score12" score function by default (the combination of "standard.wts" and "score12.wts_patch")
2. with the 'hpatch' solubility score term
Does anyone has the experience of running fixbb using these two weights? Which one is better? Thank you

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some "COMMAND ERROR" while installing rosetta2.1.0

I am trying to install Rosetta++2.1.0
and I changed the options.settings file to be compatible with gccc 4.5 which is in my my CYGWIN
but I am getting the following big error.

I will be very grateful if somebody could suggest a solution:

cygwin warning:
MS-DOS style path detected: C:\Documents and Settings\All Users\Application Da ta\scons/site_scons

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Does comparative modeling works for membrane proteins

Dear all,

Does comparative modeling works for membrane proteins?
I found a application called "topology broker" in the documentation on "TopologyBroker_GPCR" included in "protocol_capture-3.3" bundle. According to the abstract, this protocol has been used for modeling of metabotropic glutamate receptor subtype 5 protein using GPRC crystal structures. But the "flags" is only for rebuilding loops of a membrane protein whose crystal structure is known.

Does anyone know exactly how to use this?

-Justin Zhang

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Bug with make_pose_from_sequence when incorporating non-standard ResidueTypes in PyRosetta

I've been trying to assemble a poly-peptoid sequence using the make_pose_from_sequence function, however there seems to be an error in the way the polymer gets connected in the pose. For instance, the command:

make_pose_from_sequence(pose, "AAX[P02]AA", "fa_standard")

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Residue_energy_breakdown utility

I am planning to analyze residue interactions using residue_energy_breakdown utility as written in the documentation. However I could not find "residue_energy_breakdown" command in rosetta_source/bin.

I've built Rosetta3.3 in RedHat 5.4 by "scons bin mode=release" and build seemed to be finished without any problem.
Should I do any other things to use residue_energy_breakdown?

Thank you,

Post Situation: 


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