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Enzyme design with variable CST blocks possible?

Submitted by petrikigor on Thu, 2011-10-06 11:24

I am wondering if it is possible to use the enzyme design algorithm with a cst file containing variable cst blocks used for matching. I am using the following cst file for my matching:


#block 1 - Malimide-Cys
CST::BEGIN
TEMPLATE:: ATOM_MAP: 1 atom_name: C1 C2 H1
TEMPLATE:: ATOM_MAP: 1 residue3: HAS

TEMPLATE:: ATOM_MAP: 2 atom_name: SG CB CA
TEMPLATE:: ATOM_MAP: 2 residue1: C

CONSTRAINT:: distanceAB: 1.85 0.20 240.00 1 1
CONSTRAINT:: angle_A: 105.00 10.00 58.00 360.00 1

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Rosetta 3 - Applications

-kill_hairpin error

Submitted by jadolfbr on Wed, 2011-10-05 18:53

Hi.

I'm trying to use the Abinito application, and I keep getting a kill_hairpin error when I use the .psipred_ss2 file generated with fragments in robetta. Has anyone experienced this? I'm using rosetta3.3 (newest).
I'm also using the flag -psipred_ss2 with no errors...and...Both point to the same .psipred_ss2 file.
This is the error:
ERROR: [ERROR] Unknown file type for kill_hairpins file (need psipred_ss2 or kill)
ERROR:: Exit from: src/core/scoring/SS_Killhairpins_Info.cc line: 358

Thanks!

-Jared

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Rosetta 3 - Applications

-fake_native Error - not found in command line of rosetta 3.2.1

Submitted by vsjasion on Wed, 2011-10-05 12:01

Hi All,

So, I am trying to set up my docking experiment between two proteins.
I had read that for blind docking one should use the flag: -fake_native.
When I do this, I get the error: "Option matching -fake_native not found in command line top-level context"

Does this mean that "-fake_native" is no longer a flag option? And if so, is there a flag to replace it?

Thanks

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Rosetta 3 - General

[SOLVED]core.io.silent: [ WARNING ] ...

Submitted by fred on Wed, 2011-10-05 07:38

Hi List,
When clustering, I've got thousands of the following warning message:
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! Attempting to continue ...
core.io.silent: [ WARNING ] (in residue 287 natoms_pose=7atm_seqpos 287 natoms_struct=11)
core.io.silentKilled

Before clustering, I have gathered several silent files using the full atom mode with the option "silent_struct_type binary". Is there something to do with the structure type?

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Rosetta 3 - Applications

Information about “membrane_highres_Menv_smooth.wts”

Submitted by Groros on Sun, 2011-10-02 03:59

Hi there,
I would like to use the weights membrane_highres_Menv_smooth.wts as it seems to be suitable for membrane proteins. Unfortunately I can’t find any further information, could anyone help me out? A paper or any other reference would be perfect.
Many thanks

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Rosetta 3 - General

input_pdb

Submitted by evo_umich on Sat, 2011-10-01 14:20

Hi there,

I got this error when I ran pyrosetta. Any ideas? Thanks in advance!

>>> pose = Pose("test_in_short.pdb")
Traceback (most recent call last):
File "", line 1, in
Boost.Python.ArgumentError: Python argument types in
Pose.__init__(Pose, str)
did not match C++ signature:
__init__(_object*, core::pose::Pose src, unsigned long residue_begin, unsigned long residue_end)
__init__(_object*, core::pose::Pose src)
__init__(_object*)

I downloaded 3ihw and parse all lines with ATOM as one of the tutorial script taught.
My pdb file is like:

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PyRosetta - General

How to deal with Cu-as a ligand or as part of the receptor?

Submitted by hanypao on Fri, 2011-09-30 18:50

Nowadays,I try to model a Tyrosine,pdb name is 2y9w,there are two Cu exists int the protein. I checked the database and found that there's no cu atom so there's also no cu params file. So i trid to make a Cu params file manually, and add Cu atom in the database,but i don't understand (NAME ATOM LJ_RADIUS LJ_WDEPTH LK_DGFREE LK_LAMBDA LK_VOLUME)in the file "rosetta-3.2/rosetta_database/chemical/atom_type_sets/fa_standard/atom_properties.txt".what the data should i add for cu and what other files should i change. Besides,what should i deal with Cu,as a ligand or as a part of receptor?

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Rosetta 3 - General

loop modelling error on Rosetta3.2 or Rosetta3.3

Submitted by exchhattu on Thu, 2011-09-29 03:58

I am trying to remodel the loop giving low-resolution electron density map. I have tried Rosetta3.2 and 3.3 however the job could not complete when I run in mpi mode. Could you have any solution for this?

The log of error is like this. It is due to mpi.

output filename: .//outdir_2/S_0003.pdb
ERROR: Unable to open file: .//outdir_2/S_0003.pdb
ERROR:: Exit from src/protocols/jobdist/JobDistributors.cc line:727

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Rosetta 3 - General

AbinitioRelax Disulfide Bonds are not being retained

Submitted by brspurri on Wed, 2011-09-28 13:55

Hi All,

I am using Rosetta AbinitioRelax, and for the most part, it seems to be going alright. However, when I introduce a disulfide bond, the application executesas normal, yet does *not* seem to retain the disulfide bond. I have seen this complication elsewhere on this forum, but there doesn't seem to be any correct advice on how to solve the problem.

My flags are:
-database $DATABASE
-in:file:fasta sequence.fasta
-in:file:frag3 fragments.3
-in:file:frag9 fragments.9
-in:fix_disulf disulfide.ss
-in:file:fullatom
-out:nstruct 10000
-out:file:silent structures_silent.out

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