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cluster error

I've generated one PDB file containing several strucrues of the same protein MD trjactory by VMD. I try to use the cluster protocol to cluster my structure, but it is always says: the PDB format can not recognize by Rosetta. I also split the one file into different indivisual structural files, but the error is still there.Could you please give me some advices for this issue?
Thank you very much.

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Bug in ?

It seems that there is a bug in When I use this mover in my protocol, my programme exit with en error from BackrubMover::add_segment() function (input pose is null). So I read the code and found that the author may forget to set the input pose. I added two line codes after line 135 in Now it works.

line 134: protocols::moves::BackrubMover backrubmover;
line 135: backrubmover.branchopt().read_database();

/////////////////////my codes//////////////////////////////////

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general question about protein docking

I am wondering what's the general steps for Rosetta protein docking. I found there are two methods people usually use for protein docking by rosetta:

Method one:
low resolution docking(only backbone)-->cluster-->high resolution docking

Method two:
low resolution docking(only backbone)-->cluster--> relax (add sidechain with full atoms)-->high resolution docking

I am wondering which one is much more reliable?

Thank you very much

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Loop modeling with ligand in the receptor

I have docked ligand in a receptor and now I want to perform a loop modeling. I tried using these flags:
-in::file::extra_res_fa aral.params
-loops::extra_res_fa aral.params
... but rosetta returns; ERROR: Option matching -in:extra_res_fa not found in command line top-level
Without these flags Rosetta returns:
ERROR: unrecognized aa ARE
(ARE is my ligand).

So, how do I get loopmodel to recognize my ligand?


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build error in HotspotStub.os in Rosetta 3.1


I used Fedora 14 with all updates. When I got the new version of it build okay until this points. I think there might be error in the optimalization either in Gcc or Rosetta. I have this email knutjorgen(at) Do you think I should open a bug in Fedoras bugdatabase,


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Units of kT for MC mover

Hello, I'm wondering how we can connect the values for kT specified for an MC mover, to a real world temperature and Boltzmann's constant. As per this post:
Tue, 07/07/2009 - 10:37
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Rosetta reports energies in Rosetta Energy Units.

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Fold tree not correct for multi-chain partners

I have a two partner docking problem, where the first partner is made up of chains A,B,C,and D, and the second partner is chain X. They are loaded from a single PDB.

In my script I am using:

dock_prot = DockingProtocol()
print p.fold_tree()

Which prints:

FOLD_TREE EDGE 1 117 -1 EDGE 117 118 1 EDGE 118 227 -1 EDGE 227 235 -1 EDGE 227 479 4 EDGE 235 236 2 EDGE 236 353 -1 EDGE 353 354 3 EDGE 354 471 -1 EDGE 479 472 -1 EDGE 479 486 -1

However, once the pose is created, a command such as:


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