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computer specifications

Submitted by rlwoltz on Tue, 2012-10-09 16:11

I am buying a computer specifically to run protein folding predictions and protein docking predictions. I am using a computer now that has 4GB of RAM and a 3.33 Ghz processor. However I seem to be running out of memory on some of the models, I can only run one or maybe two at a time, and the abinitio algorithm for a 80 aa protein takes 3 weeks for 10000n. Does anyone know what the recommended size and specs for a decent computer to do this work using Rosetta 3.4 would be?

Thanks
Ryan

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Rosetta 3 - General

Problem with AtomPair constraint

Submitted by jarek on Tue, 2012-10-09 07:28

Dear all,

I am doing protein-protein docking. To limit myself to a particular docking site I use the following site constraint:
SiteConstraint CA 521A S FLAT_HARMONIC 0 1 5
This works perfectly fine, and I'm getting poses only around the residue 521A.

Later on, I decided to restrict my poses to only the ones that have a particular
aminoacid contact between chain A and S. I changed the constraint file to:
AtomPair CA 521A CA 13S HARMONIC 6.23 2.0

what I'm getting now is the following error message:

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Rosetta 3 - Applications

segmentation fault after core.kinematics.FoldTree in homology modeling

Submitted by pdbb on Mon, 2012-10-08 14:27

Hi, as I perform homology modeling, I get a 'segmentation fault' message. Following is my output right before the error message. Why could this be happening and what I could do to solve it? Thank you for any insights.

......
protocols.looprelax: Repacking because in loop: 387
protocols.looprelax: Repacking because in loop: 388
protocols.looprelax: Repacking because in loop: 389
protocols.looprelax: Missing dens: 389
protocols.looprelax: Repacking required
protocols.looprelax: Detecting disulfides

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homology modeling with end extension

Submitted by fred on Mon, 2012-10-08 14:19

Hi there, I'm running the "homology modeling with end extension" to the model region between two subdomains of a protein. The first subdomain has ~100 aa and it structure has been solved by NMR; the second subdomain has ~200 aa and has been solved by X ray. The region between them has about 120 aa long accompanied by a poor SS prediction. How many aa such script can deal with?

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Rosetta 3 - Applications

FlexPepDock for protein containing multiple chains

Submitted by Dimitrov on Mon, 2012-10-08 08:31

Hi,
I try to dock a peptide to a protein containing two chains using "flexpep" protocol.
Is it necessary to rename and renumber the second chain in my protein to have the same chain ID as the first one?
Or there is some option to specify the ID of the two chains as a receptor and the ID of the peptide as a ligand?

Thanks

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Rosetta 3 - Applications

ddG backbone movement

Submitted by dave on Wed, 2012-10-03 03:23

Hello,
I am using Rosetta 3.3, ddg_monomer application. I am trying to reproduce protocol 19 from Table I (Kellog, 2010) but it looks like there is no backbone minimization at all. In Fig. 3 there is a visible backbone movement but in my case it behaves like in supplementary material Fig. 1, where no backbone movement is observed.

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Rosetta 3 - General

homology modeling- Error: length mismatch between sequence and alignment.

Submitted by pdbb on Mon, 2012-10-01 07:57

Hi,

As I run homology modeling on Rosetta 3.4, I get an error message: "Error: length mismatch between sequence and alignmentproblem with sequence:" I checked my input files and the script of SequenceAlignment.cc that produces the message. My files seem to be fine. I am using general format for alignment file. My question is, what sequences are being compared to produce this message. Thanks.

Here is an excerpt of script:

void SequenceAlignment::data_integrity_check() const {
for ( Size jj = 1; jj <= size(); ++jj ) {
if ( sequences_[jj]->length() != length() ) {

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Enzyme design output silent file and score file

Submitted by deltag on Fri, 2012-09-28 13:07

Hi Rosetta Users,

A quick question. can enzyme design output silent and score files if I chose to output multiple models? I tried to add the following flags but didn't have the silent and score files. Only individual pdb files were output.

-out:file:silent design.out
-out:file:scorefile design.sc

Thanks for help.

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Rosetta 3 - Applications

Identical decoys

Submitted by aroop on Tue, 2012-09-25 12:50

Hi!

I am trying to repack two residues in a protein using the following command line:
/Users/aroop/rosetta31/bin/fixbbSym.macosgccrelease -database /Users/aroop/rosetta31/rosetta_database/ -in:file:s 213N_215S.pdb -symmetry:symmetry_definition s769.sdef -symmetry:initialize_rigid_body_dofs -resfile s769_213N_215S.resfile -nstruct 100 -out:file:scorefile s769.score12 -packing:ex1 -packing:ex2 -packing:ex3 -packing:ex4 -packing:ex1aro -packing:ex2aro -packing:ex1aro_exposed -packing:ex2aro_exposed -packing:ex1:level 4 -packing:ex2:level 4 -packing:ex3:level 4 -packing:ex4:level 4

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