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FlexPepDock and total score problem

Submitted by tkellici on Fri, 2014-01-17 06:07

I've used the FlexPepDock server to dock a small peptide of 8 residues into a homology model I've build. Everything went fine but I've become worried by the total score that seems to be a big positive number. The data.txt is this:

total_score rmsBB description
557.705 27.104 top_1.pdb
566.033 18.824 top_2.pdb
689.012 2.691 top_3.pdb
700.556 3.081 top_4.pdb
720.698 2.056 top_5.pdb
721.482 2.797 top_6.pdb
725.492 3.496 top_7.pdb
734.544 2.646 top_8.pdb
740.963 1.671 top_9.pdb
742.097 3.046 top_10.pdb

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Rosetta 3 - Applications

Fastrelax energy

Submitted by Lindsay on Thu, 2014-01-16 21:04

Dear all,
I am relaxing a pdb using fastrelax of rosetta_2013_week51 and I found something strange.
my 1st command line is:
./relax.linuxgccreleas ../rosetta_database/ -relax:constrain_relax_to_start_coords -relax:coord_constrain_sidechains -relax:ramp_constraints false -s test.pdb -ex1 -ex2 -use_input_sc -flip_HNQ -no_optH false -ignore_zero_occupancy false -overwrite -constant_seed -jran 1111111 -relax:fast

the energy of relaxed structure is -56.1966

the 2nd command line is:

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Rosetta 3 - General

Scoring a membrane protein in PyRosetta?

Submitted by tsikosek on Thu, 2014-01-16 15:05

Hi everyone,

I would like to study mutations in a membrane protein with PyRosetta. Is this currently possible and if so, how do I pass on information about the transmembrane region to the scoring function?
Should I use the 'score_membrane.wts' scoring function?

Thanks,
Tobias

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PyRosetta - Applications

install in AMD cluster

Submitted by albumns on Wed, 2014-01-15 02:16

Hello:

I am trying to install rosettat-3.5 in a AMD based cluster with command:

scons bin extras=mpi mode=release

but it failed with messages:

-----------------------------------------------------------------
scons: Reading SConscript files ...
Copy("user.options", "user.options.template")
Copy("user.settings", "user.settings.template")
Copy("/home/users/albert/install/rosetta-3.5/src/pilot_apps.src.settings", "/home/users/albert/install/rosetta-3.5/src/pilot_apps.src.settings.template")
Traceback (most recent call last):

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Rosetta 3 - Build/Install

Compiler error - libcore.3.a GeometricSolEnergy

Submitted by Robert on Tue, 2014-01-14 13:36

I'm trying to compile a fresh install and I get this error.

Anyone seen this before?

build/src/release/linux/2.6/64/x86/gcc/4.5/static/libcore.3.a(ContextIndependentGeometricSolEnergy.o): In function `core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::residue_pair_energy_ext(core::conformation::Residue const&, core::conformation::Residue const&, core::scoring::ResPairMinimizationData const&, core::pose::Pose const&, core::scoring::ScoreFunction const&, core::scoring::EMapVector&) const':

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Rosetta 3 - Build/Install

Protein docking with PyRosetta Error!

Submitted by Apiwat on Sat, 2014-01-11 23:32

Hi, I'm new PyRosetta user. I'm trying to dock 2 protein by usig D100_Docking.py script. I started with relax these two protein and then combinded into the same file separated by TER line. I aim to generate 1000 decoy first, but ,after run the script, it's always terminated by below error

ERROR: NAN occurred in H-bonding calculations!
ERROR:: Exit from: src/core/scoring/hbonds/hbonds_geom.cc line: 1187

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PyRosetta - General

Clustering Rosetta output PDB files

Submitted by ritacc18 on Sat, 2014-01-11 20:13

Hi,

I'm using Rosetta ~10,000 PDB output and using cluster software Calibur to cluster it.
And question occurs to me, is that, are the alpha carbon RMSD for each clusters, were calculated after all the PDBs are superimposed? or were RMSD calculate before they are superimposed, to represent the most popular states in space? (either answer about Calibur or Rosetta's own cluster application will be very helpful!)

Because my RMSD for each cluster is very large ~10 Angstrom, which should ideally < 2 angstrom to get a close to native structure, right?

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Rosetta 3 - General

extraction of pdbs from silent.out files on Mac

Submitted by pramod on Tue, 2014-01-07 11:43

Hi RosettaCommons support group,

I have generated silent.out files using Rosetta 3.5 version to build homology models. I tried to extract the pdbs using the following script:
~/rosetta-3.5/rosetta_source/bin/extract_pdbs.macosgccrelease -database ~/rosetta-3.5/rosetta_database/ -in:file:silent silent.out -in:file:silent_struct_type binary -out:file:residue_type_set fa_standard, but could not and the error is as follows:

core.init: Mini-Rosetta version Split from developer trunk at 53488 from http://www.rosettacommons.org

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Rosetta 3 - General

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