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cluster error

Hello:
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.

Post Situation: 

Bug in LoopMover_Refine_Backrub.cc ?

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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general question about protein docking

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

Post Situation: 

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?

Thanks,
Christoffer

Post Situation: 

build error in HotspotStub.os in Rosetta 3.1

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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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
#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.

Post Situation: 

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()
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)

Post Situation: 

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