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Random seed confusion

Submitted by pardave on Mon, 2012-11-12 09:45

I have seen several commands for Abinitio recently using the -constant_seed and -jran options.
Normally I don`t use MPI for my jobs but instead submit, say, 100 jobs each producing 1000 decoys. Each job will run on a single processor.
Am I correct in thinking that it should not be necessary to specify these parameters?
cheers
D.

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Rosetta 3 - General

missing ram_buildloop_wrapper4.pl in rosetta antibody modeller

Submitted by jchin on Sun, 2012-11-11 19:31

Rosetta 2.3.0
Python 2.4.3
Run on cluster

I'm attempting to setup rosetta antibody but encounter the error message below( script ram_buildloop_wrapper4.pl is missing).
My installation is rosetta 2.3.0. The script doesn't seem to be in rosetta++ or rosetta3 either.
[…@login-0-0 test]$ perl -P ../antibody/scripts/ram_buildloop_wrapper4.pl ../antibody/database/pdb1xyz_chothia.pdb bit ram ram 1 1 1 1 1 0 0 1 1 0 0 0 0 FR 02 2 1 3 2000 2000 3 0 ../1dqq_h.fasta 1dqq_l.fasta

/home/…/immunity/test

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Rosetta++ - Applications

Question regarding buried or exposed residues

Submitted by qlj on Fri, 2012-11-09 23:43

Dear all,

I'd really like to know which application can define the residues of a protein to be burrei or exposed in Rosetta3.4. I could not find this piece of information in the manual. I need your help to introduce the details including the commond and related flags(I find some thing at http://www.rosettacommons.org/content/question-regarding-mlipo-score , but I didn't konw it meets my requirement and how the .lips4 file is produced).
Thanks for your help.

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Rosetta 3 - General

Write one's own constraint type

Submitted by djpittdj on Thu, 2012-11-08 12:29

Hi, everyone:
I wonder if there's a template/example source code file in Rosetta from which we can build our own type of constraint. For example, when docking B against A, both are helices, A is fixed and one wants to constrain the tilt angle of B with respect to the z-axis, how can I do this besides blind docking followed by post-processing.
RosettaScript seems like a good candidate but it does not have this kind of utility.
And is there a programming guide for Rosetta?
Thanks a lot.
Jian

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Rosetta 3 - Applications

membrane ab initio modeling application with constraints

Submitted by ytao on Thu, 2012-11-08 11:56

Hi,

I'm trying to use the membrane ab initio modeling application (membrane_abinitio2). I have followed the instructions in the "membrane_abinitio" demo directory and it did work.

My question is: can I add constraints (such as disulphide bonds) and NMR restraints (such as RDC measurements) in the process?

I tried to add -fix_disulf and -score:patch flags in the command but it didn't seem to affect the outputs. The score file did not have "rdc" terms in it and the structures did not satisfy the disulphide bonds.

Thanks,

Yisong

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Rosetta 3 - Applications

fixbb and ncaa's

Submitted by jarek on Thu, 2012-11-08 04:55

I am trying to use the fixbb application with non-canonical amionoacids.
I have prepared a test res file:

NATRO
start
23 B EMPTY A20 B47 B48

and use the -score:weights mm-std flag
I have also de-commented the l-ncaa aminoacids in the chemical/residue_type_sets /fa_standard/residue_types.txt

now when I run it, I get this:
core.pack.task.ResfileReader: On line 3 command 'A20'is not recognized

Do I need to do anything else to have the ncaa's available for fixbb ?

Thanks

Jarek

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Rosetta 3 - Applications

protein docking failed

Submitted by albumns on Thu, 2012-11-08 02:59

hello:

I am docking a two proteins: one is with 900 aa the the left is 200 aa. here is my protocol:

/home/albert/install/rosetta3.4/rosetta_source/bin/docking_protocol.linuxgccrelease \
-database /home/albert/install/rosetta3.4/rosetta_database \
-nstruct $nstruct \
-s ../input.pdb \
-docking:docking_local_refine true \
-docking:dock_pert 3 8 \
-docking:spin true \
-docking:dock_min true \
-ex1 \
-ex2 \
-out:path:pdb ./ \
-out:suffix $i \
-out:file:fullatom \
-out:pdb \

the job failed with messages:

ERROR: total_residue() != 0

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Rosetta 3 - Applications

fix the left part doesn't work

Submitted by albumns on Wed, 2012-11-07 00:02

hello:

I am using the following protocol which someone used in the forum to build loop based on crystal structure. I am going to fix the left part of the region since they are from crystal structure and I find that all the regions are rebuild by Rosetta. I am just wondering, where is the problem?

thank you very much

/opt/rosetta3.4/rosetta_source/bin/loopmodel.default.linuxgccrelease \
-database /opt/rosetta3.4/rosetta_database \
-nstruct $nstruct \
-loops:input_pdb ../crystal.pdb \
-loops:loop_file ../input.loop \
-loops:remodel perturb_kic \
-loops:refine refine_kic \

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Rosetta 3 - Applications

rosetta compilation error

Submitted by jarek on Tue, 2012-11-06 04:05

I am trying to build rosetta on a cluster that is running SUSE 2.6.16
I use scons supplied with the rosetta 3.4 package.
In rosetta_source I run this command: external/scons-local/scons.py bin mode=release

At first everything seems to be working, it keeps on compiling for 1 hour and then I get the message below.
Any idea what could have gone wrong ?

Jarek

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Rosetta 3 - Build/Install

model protein at low pH

Submitted by ytao on Mon, 2012-11-05 07:52

Hi,

I'm a noob in rosetta modelling. I need to model my protein at low pH, i.e. with protonated Asp and Glu residues. How should I setup the simulation(ab initio and relax)?

I found there are residue type files for fullatom protonated Asp and Glu in rosetta_source directory, but I don't know how to use them:(

Thank you very much,

Yisong

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Rosetta 3 - General

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