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unwanted Glycines after PackRotamersMover

Submitted by oppopomoz on Tue, 2014-03-04 10:08

Hello everybody.

I am trying to design the sequence of small peptides (4-8 aa long) using PackRotamersMove but I tend to get way too many glycines (50% of residues become Glycines as avarage).
here my protocol:

"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
scorefxn_12 = create_score_function_ws_patch('score12','score12')
task_design = TaskFactory.create_packer_task(pose)
parse_resfile(pose, task_design,"resfile")
pack_design = PackRotamersMover( scorefxn_12, task_design )
pack_design.apply(pose)
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

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PyRosetta - Scripts

InterfaceAnalyzer problem

Submitted by almeida on Mon, 2014-03-03 14:56
Hi all, I'm trying to run InterfaceAnalyzer in the "classical" and xml script modes. In the "classical" mode I ran: > InterfaceAnalyzer.linuxgccrelease @flags_IL2_Q74P_2 ... with this flags: -in:file:l ../IL2_IL2Ra_new_0001.pdb -in:file:fullatom -compute_packstat true -tracer_data_print true -out:file:score_only score.sc -use_resfile yes -resfile IL2_Q74P.resfile -fixedchains A B -pack_input false -pack_separated true -add_regular_scores_to_scorefile true -use_jobname true -database /home/almeida/Softwares/Rosetta/rosetta_3.4/rosetta_database
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Rosetta 3 - Applications

error while loading shared libraries: libmpi_cxx.so.1

Submitted by tevang on Fri, 2014-02-28 05:35

Greetings,

I encounter a strange error when I try to run minirosetta on a cluster. Although compilation appears to finish successfully, minirosetta does not find a library that exists. This is how I run it:

module purge
module load OpenMPI/1.4.5-GCC-4.6.3
export PATH=/gpfs/h/lspro220u2/Opt:/gpfs/h/build/eb131021/software/OpenMPI/1.4.5-GCC-4.6.3/bin:$PATH
export LD_LIBRARY_PATH=/gpfs/h/build/eb131021/software/OpenMPI/1.4.5-GCC-4.6.3/lib:$LD_LIBRARY_PATH
export INCLUDE=/gpfs/h/build/eb131021/software/OpenMPI/1.4.5-GCC-4.6.3/include

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Rosetta 3 - Build/Install

Determining Rosetta version from directory

Submitted by linucks on Fri, 2014-02-28 04:04

Hello,

I develop some software that runs Rosetta and need to know what version of Rosetta is being used so that it can set flags etc. appropriately.

Ideally I need to be able to determine the version of Rosetta when I am just given the path to the top-level directory.

In previous versions of Rosetta there was a README.version file that contained this information. Unfortunately this has now disappeared and I can't find anything else suitable.

Does anyone have any suggestions of the best way to determine the version?

Thanks,

Jens

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Rosetta 3 - General

Resfile

Submitted by vijayaraj81 on Thu, 2014-02-27 01:14

Hello,

I am using Rosettascripts (version 3.5) to redesign the protein-protein interface, I use the following applications to redesign the interface,
1. Minmover - for energy minimization
2. PackrotamersMovers - for repacking and redesigning of interface residues
3. set of filters to filter the output

I would like to apply some restrictions on the amino acid selection during the redesing process which are,
1. retain the native ALA amino acids while redesigning and
2. do not substitute ALA aa while redesinging

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Rosetta 3 - General

Rotamer bin vector from chi angles of a residue in pose not found in Dunbrack rotamer library

Submitted by AyushGoyal on Mon, 2014-02-24 22:18

I calculate the rotamer vector for a residue in a specific position in a pose using the rotamer_from_chi function with the following code:

rota = RotamerFromAngles(pose, moltenresid);

def RotamerFromAngles(pose, residue_number):
residueType = pose.residue_type(residue_number);
angles = pose.residue(residue_number).chi();
rotv = rosetta.utility.vector1_Size();
rotamer_from_chi(residueType,angles,rotv)
print 'Residue type: ', pose.residue(residue_number)
print 'Residue chi angles: ', angles
print 'Residue rotamer vector: ', rotv
return rotv

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PyRosetta - General

cluster.mpi.linuxgccrelease failed

Submitted by fred on Mon, 2014-02-24 12:11

Hi there,
I was clustering a silent files with my 10% lowest energy decoys and the cluster.mpi.linuxgccrelease just stopped and issued the following on screen:

--------------------------------------------------------------------------
mpirun noticed that process rank 4 with PID 19956 on node compute-1-5 exited on signal 9 (Killed).
--------------------------------------------------------------------------

Well, it seems some problem with MPIRUN rather than with the cluster.mpi.linuxgccrelease binary.
I'm running cluster.mpi.linuxgccrelease with the following command line:

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Rosetta 3 - Applications

Number of conformations needed

Submitted by JadAbbass on Sun, 2014-02-16 13:21

Dear Sir,

Q1) For a <100 residues protein, is it "enough" to generate 20,000 structures before comparing/clustering?
Q2) (I apologize if the question is beyond this forum) Is(Are) there nay formal publication(s) that mention directly/indirectly the "minimum/typical" number of conformations needed?

Thank you in advance,
Jad

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Rosetta 3 - General

make_fragment.pl Error!

Submitted by Apiwat on Sat, 2014-02-15 13:35

Hi all,

I want to generate fragment for using in homology modelling. After I installed all tools and database by the script make_fragments.pl -verbose 1NB1.fasta , I found this error.

nr_pfilt database missing so using nr: /home/nong/Documents/Rosetta/rosetta_2013wk52_bundle/tools/fragment_tools/databases/nr
no id specified. parsing filename instead.
cannot parse id from filename so using 't001_'
ID: t001 CHAIN: _
File for psipred not found! Generating from scratch instead.
picking fragments with options:
DEBUG: 1
add_pdbs_to_vall:

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Rosetta 3 - General

How to calculate the binding energy of peptide and a protein?

Submitted by tianbu on Thu, 2014-02-13 20:44

I have lots of peptides and a protein as a complex structure. Is there any way for me to calculate the binding energy of them? Basically I want to see which peptide will have stronger binding with the protein. I don't need to dock since I already had the complexes. Thank you very much!

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Rosetta 3 - General

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