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error with profit

Submitted by jchin on Thu, 2012-11-15 10:00

Hi,

I get an error below with profit being called on profit.in

Scan one or more sequences with a simple frequency matrix
Profile or weight matrix file: Error: Unable to open file 'QUIET' for input
Profile or weight matrix file: Error: Unable to open file 'ZONE CLEAR' for input
Died: profit terminated: Bad value for '-infile' and no more retries
256 at /home/.../immunity/antibody/scripts/ram_buildloop_wrapper4.pl line 12

__

The contents of profit.in (below), don't seem to match the expected input for profit.

QUIET
ZONE CLEAR
ATOMS CA
templatelightheavy.pdb queryL.pdb

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Rosetta++ - Build/Install

P-P docking with suitable constraint type

Submitted by Yao Wu on Tue, 2012-11-13 18:03

Hi, I've a question about protein docking with constraits.
Biochemical assay proves that a specific residue pair between two monomers is for sure to be close enough, for which FlatHarmonic constraint type can be used.
However, another 17 inter residue pairs were identified by chemical cross-linking. 1. not all these 17 pairs are reliable, some might be experimental artificial, but we don`t konw which ones. 2. Based on konwn monomer structures, we can find some of these 17 pairs can not be satisfied at the same time, indicating a plausibility of multiple binding modes.

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Rosetta 3 - Applications

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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