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gcc/scons Rosetta3.3 compile error on RHEL5, 32bit Linux, scons0.98.4, python2.6.2, gcc 4.1.2

Submitted by zigeuner on Thu, 2011-08-11 09:52

Hi guys,
I'm getting a strange error during the build process when I try to compile the new 3.3 version. I haven't had problems on the same computer/setup with previous versions. The problem appears to be that scons is passing bad commandline options to gcc, specifically a '- s t d = c 9 9' string where the spaces are giving gcc hiccups. Any ideas? I tried correcting the gcc commandline, running separately, then going back to the scons commands again. It just has a problem on the next compilation instead. Scons output is below.

thanks!

-Louis

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Rosetta 3 - Build/Install

ERROR: no fragment to compute secondary structure

Submitted by byin on Sun, 2011-08-07 23:55

Hi,im now doing the structure prediction using Abinitio way.
But when i run the command,i get this error:
ERROR: no fragment to compute secondary structure
ERROR:: Exit from: src/core/conformation/SecondaryStructure.cc line: 67

in my input files there,i already included :aat000_03_05.200_v1_3.rtf, aat000_09_05.200_v1_3.rtf and the fasta file as well...

So may i know what is the problem?

tq!

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Rosetta 3 - Applications

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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