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Bug in LoopMover_Refine_Backrub.cc ?

Submitted by SunH on Wed, 2010-12-15 00:08

Hi,
It seems that there is a bug in LoopMover_Refine_Backrub.cc. 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 LoopMover_Refine_Backrub.cc. Now it works.

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

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

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Rosetta 3 - General

general question about protein docking

Submitted by albumns on Mon, 2010-12-13 23:26

Hello:
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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Rosetta 3 - General

Loop modeling with ligand in the receptor

Submitted by cno on Mon, 2010-12-13 14:07

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?

Thanks,
Christoffer

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Rosetta 3 - General

build error in HotspotStub.os in Rosetta 3.1

Submitted by knutjbj on Sat, 2010-12-11 03:02

Hi

I used Fedora 14 with all updates. When I got the new version of sasa.cc 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)gmail.com. Do you think I should open a bug in Fedoras bugdatabase,

gcc-4.5.1-4.fc14.x86_64
glibc-2.12.90-19.x86_64
gcc-c++-4.5.1-4.fc14.x86_64

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Rosetta 3 - Build/Install

Units of kT for MC mover

Submitted by msellers on Fri, 2010-12-10 05:40

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
#1
smlewis
User offline. Last seen 9 hours 49 min ago. Offline
Joined: 08/04/2010
Contact user

Rosetta reports energies in Rosetta Energy Units.

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PyRosetta - General

Fold tree not correct for multi-chain partners

Submitted by msellers on Fri, 2010-12-10 05:35

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()
dock_prot.setup_foldtree(p,'ABCD_X')
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:

p.pdb_info().pdb2pose('X',1)

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PyRosetta - General

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