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Using D-amino acids in Rosetta docking

Submitted by moehle on Wed, 2011-06-01 00:49

Hi,

I have tried to use the docking protocol of Rosetta3.2.1 for docking of well structured peptide to protein receptor. The peptide contains the D-amino acids(D-Pro, D-Arg). The corresponding "params" files are located in "residue_types/d-caa"

First I changed the related lines in "residue_types.txt", to get the params files active. The residue types seem to be recognized by Rosetta but it fails with the following error message

ERROR: unknown atom_name: DPR H
ERROR:: Exit from: src/core/chemical/ResidueType.cc line: 1454

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Rosetta 3 - General

installation using scons on cygwin

Submitted by isengupta13 on Tue, 2011-05-31 11:50

Hi
I have been trying to install rosetta v2.3 on my laptop which has the windows xp operating system. I have installed cygwin as well as scons. When I type scons mode=release in the rosetta++ directory I get the following error:

scons: Reading SConscript files ...

scons: warning: The Options class is deprecated; use the Variables class instead.
File "/usr/local/rosetta/rosetta++/tools/build/setup.py", line 32, in setup_build_options

scons: warning: The EnumOption() function is deprecated; use the EnumVariable() function instead.

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Rosetta++ - Build/Install

protein structure prediction using relax -- high-powered jobs

Submitted by rfieldhouse on Mon, 2011-05-30 18:29

Quick question, I am interested in refining a few homology models with long runs of the relax protocol. I find the run time is fairly short on my local supercomputer system, and I'd like to make maximum use of the resources available to me. So, how do I improve my models by refining for a week instead of just a few minutes without having the job exiting? (Note: I believe the run exits normally.)

Also, is there a good order to use the applications when it comes to relax / loop modeling / backrub?

Thanks,

Rob

***

My command:

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Rosetta 3 - Applications

Rosetta3.2.1-Intel-11.

Submitted by ravichandrans on Wed, 2011-05-25 09:16

Hello Rosetta Developers:

Rosetta: 3.2.1
Compiler: Intel 11.1.072
Python: 2.7
OS: Linux x86_64

Compilation aborts with the following message. Is there a patch available for this one?
Thanks
Ravi

-------------------------------------------------------------Compilation output-----

./scons.py compiler=icc bin mode=release
scons: Reading SConscript files ...
svn: '.' is not a working copy
scons: done reading SConscript files.
scons: Building targets ...

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Rosetta 3 - Build/Install

How to model a protein that dimerizes to a small molecule?

Submitted by pholland on Wed, 2011-05-25 07:29

I have a protein that dimerizes to a GAG molecule, and I would like to model the dimerization to the GAG using Rosetta. I have attempted to use Rosetta Docks to calculate the interaction; however, the GAG molecule is removed from the PDB files. First question is should I be using RosettaLigand, and if so is RosettaLigand able to model ligand binding to two protein molecules? Would it be best to take the model from RosettaDock for a RosettaLigand run with the GAG compound? Thank you for your assistance.
Cheers,

Paul Holland, Ph.D

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Rosetta++ - General

Minimization question

Submitted by rfschleif on Wed, 2011-05-25 06:59

In a two domain protein, I randomize the phi and psi angles of the interdomain linker and then energy minimize, considering only repulsive VDW. Oddly, about one third of the time, the minimization step increases the energy. Possibly the minimization function is considering only the residues that are allowed to move, but that that score function is considering the entire system. If this is what is going on, it is not what I expect or want, I'd like the minimization function to consider the entire system. Below is the python script.

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PyRosetta - General

Rosetta3.2.1-LAM-MPI Run-Problem-More than 2 processor Jobs

Submitted by ravichandrans on Tue, 2011-05-24 08:24

Hi All:

I am a new Rosetta user. I had just finished compiling parallel Rosetta (rosetta3.2.1/gcc-4.4.3/LAM-MPI-7.1.4)
and can run 2 processor jobs with no issues. But jobs fail for more than two processors (error message below).
Any help would be greatly appreciated.

Thanks

Ravi

Linux System:
-------------

Linux node2n29 2.6.32-29-server #58-Ubuntu SMP Fri Feb 11 21:06:51 UTC 2011 x86_64 GNU/Linux

Parallel version of Rosetta was compiled using GCC/LAM-MPI-7.1.4

Run Command (memory used was 8 GB)
-----------------------------------

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Rosetta 3 - Build/Install

rosetta 3.2.1 installation on fedora core 6

Submitted by bharat_46010 on Sun, 2011-05-22 22:40

Hi,

I am getting the floowing errors after executing the "scons bin mode=release" command:-
===========================================================================================
scons: Reading SConscript files ...
svn: '.' is not a working copy

scons: warning: The build_dir keyword has been deprecated; use the variant_dir keyword instead.
File "/usr/local/rosetta-3.2.1/rosetta_source/SConscript", line 40, in

scons: warning: The build_dir keyword has been deprecated; use the variant_dir keyword instead.

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Rosetta 3 - Build/Install

Problem with HETATM entries in PDB file

Submitted by asmi on Fri, 2011-05-20 10:17

Hello

I am using FARNA module for RNA denovo structure prediction. Some of the PDB files contain HETATM entries like this :

HETATM 191 P CH A 10 6.803 -7.485 -7.145 1.00 0.00 P
HETATM 192 O1P CH A 10 7.379 -8.656 -7.843 1.00 0.00 O
HETATM 193 O2P CH A 10 6.942 -6.135 -7.736 1.00 0.00 O
HETATM 194 O5* CH A 10 5.232 -7.767 -6.901 1.00 0.00 O
HETATM 195 C5* CH A 10 4.807 -8.876 -6.102 1.00 0.00 C

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Rosetta 3 - General

Questions about rosetta fragment library ranking and fragment conformation sampling algorithm

Submitted by mdyini on Thu, 2011-05-19 17:34

Hi, I have some questions about fragment library used for de novo folding and loop modeling.

From what I have read, the score for ranking fragment conformations in a library consists of two parts, which are from psi-blast results and secondary structure prediction results. My questions are:

1) When performing the psi-blast that contributes to the ranking of fragment conformations in a library at one position, does the psi-blast involve the whole protein sequence or just a local region around that position?

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