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relax with resfile

Submitted by gw on Fri, 2011-08-05 10:57

the relax protocol in 3.2.1 doesn't seem to be recognizing my resfile. I want to relax my structure as close to the native as possible (rotamers, backbone) and slowly allow more freedom.

relax.mpi.linuxgccrelease -database /home/gw/rosetta3.2.1/rosetta_database/ -s input.pdb -ex1 -ex2 -use_input_sc -extra_res_fa /home/gw/rosetta3.2.1/rosetta_database/chemical/residue_type_sets/fa_standard/residue_types/water/TP5.params -relax:fast -resfile natro.txt -nstruct 250 -overwrite

Here is the resfile, natro.txt:

NATAA
start
45 A NATRO #i45
46 A NATRO
47 A NATRO #n47
48 A NATRO

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Rosetta 3 - Applications

Pairwise decomposable terms in the Rosetta energy function

Submitted by pgainza on Wed, 2011-08-03 12:26

Dear all,
I've been wanting to try out the Rosetta energy function with DEE/A* but I realize that few of the terms are pairwise decomposable.

I was wondering whether there is a parameter or a simple way to make energy terms like hydrogen bonds and electrostatics (fa_pair) context independent (e.g. make hydrogen bonds dependent only on the donor-acceptor residues).

I've seen some work on DEE/A* using the Rosetta energy function (Fromer and Yanover, Proteins 2009) but it was not clear to me how they decompose the energy function.

Thanks!!
Pablo

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Rosetta 3 - General

Rosetta 3.3 build error in RHEL 6.1

Submitted by b5foan on Tue, 2011-08-02 02:34

Trying to build Rosetta 3.3 on RHEL 6.1 64-bit machine.

gcc 4.4.5, Python 2.6.6, scons in Rosetta

admin@computer in rosetta_source: external/scons-local/scons.py -j4 bin mode=release

blah, blah, blah

src/protocols/nonlocal/NonlocalAbinitioReader.cc: In static member function 'static void protocols::nonlocal::NonlocalAbinitioReader::read(const std::string&, utility::vector1 >*)':
src/protocols/nonlocal/NonlocalAbinitioReader.cc:112: internal compiler error: Segmentation fault

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Rosetta 3 - Build/Install

busted tape archive (i.e. tar error)

Submitted by b5foan on Mon, 2011-08-01 09:48

I've just downloaded the full Rosetta 3.3 bundle (twice, to be sure), but it's not a valid tar file.

>> tar tf rosetta3.3_bundles.tgz
rosetta3.3/
rosetta3.3/Antibody-3.3.tgz
rosetta3.3/rosetta3.3_fragments.tgz
rosetta3.3/new_apps.note
rosetta3.3/protocol_capture-3.3.tgz
rosetta3.3/rosetta3.3_database.tgz
rosetta3.3/foldit-3.3.tgz
rosetta3.3/release.note
rosetta3.3/rosetta3.3_demos.tgz
rosetta3.3/BioTools-3.3.tgz
rosetta3.3/README.Copyrights
rosetta3.3/rosetta3.3_source.tgz
rosetta3.3/README.version
rosetta3.3/rosetta3.3_manual.tgz

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Rosetta 3 - Build/Install

score_jd2.linuxgccrelease documentation

Submitted by fglaser on Mon, 2011-08-01 04:08

Hi all,

I would like to get documentation about the calculation and the output of the score application, e.g. what each of the parameters exactly mean and how it is calculated, and about if it is better to add hydrogens to run score.

SCORE: score fa_atr fa_rep fa_sol fa_intra_rep pro_close fa_pair hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_ss_dst dslf_cs_ang dslf_ss_dih dslf_ca_dih rama omega fa_dun p_aa_pp ref linear_chainbreak overlap_chainbreak time description

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Rosetta 3 - Applications

Using Relax to asses conformational space

Submitted by glapidoth11 on Sat, 2011-07-30 05:09

Hi all,
I am a new user to Rosetta and i have a question regrading the relax protocol. I have been using it to create decoys for a target protein, however, I get a sense that the configurations that I am getting are too close to the original structure and so I am not getting a good enough sampling of the conformational space. Is there another protocol I can try or maybe a flag to be used inside the relax protocol to get a more rigorous sampling?
Thanks,
Gideon

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Rosetta 3 - General

protein structure prediction

Submitted by ravi1709 on Thu, 2011-07-28 00:05

I did homology modelling with Robetta server and it generated different model. When I saved the image, it was not in pdb file it was chemical/x pdb format.The file opens with Rasmol but Now I am getting difficulty with further process (Procheck)because for the a pdb format (.pdb) is needed for that and it shows a bad file format for chemical x pdb format. Kindly help me regarding this matter.

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PyRosetta - General

question about scoring silent output files and their contents

Submitted by burkheadlab on Wed, 2011-07-27 16:28

After clustering I created silent files for every cluster with the contents being the info from every structure in that cluster. I then went to score these silent files and output another silent file with the score results (one silent file for every cluster with the score values in it). My problem is that the silent file produced from running the score function contains not only the scores but also the info from the .pdbs for each structure. I would like this file to have only the score values for the structures in each cluster. Is there an easy way to accomplish this?

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Rosetta 3 - General

Using pose.set_xyz() to move chains causes increase in only pro_close energy

Submitted by msellers on Mon, 2011-07-25 06:57

I am recording the positions of all atoms before I run a Rosetta protocol + external software perturbations, and using these positions to "reset" the system after the protocals have completed. The score is computed before and after the protocols, and after resetting the system. I noticed resetting causes a large increase in the score (-1000 to 25000).

Looking at the score by residue, the culprit was pro_close for Prolines...

-My first guess is that this is an improper ring angle, except that this structure was a starting structure in Rosetta.

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PyRosetta - General

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