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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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Read more about FlexPepDock for protein containing multiple chains
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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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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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Read more about Enzyme design output silent file and score file
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homology modelling with DNA

Submitted by zadie1118 on Fri, 2012-09-28 06:35

Hi all

I'm wondering if there is a way of doing Homology modelling of a protein complexed with the DNA, is there a way to keep the DNA in the template structure? it would be already great if the DNA could be considered at occluded space.

Thanks

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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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Docking failure

Submitted by khanhbinh on Sun, 2012-09-23 22:19

I'm trying to dock 2 proteins in Rosetta dock serve (http://rosettadock.graylab.jhu.edu/) but it always has this problem:

This job failed to produce results. The RosettaDock Server support team has been notified.

Most failures result from departures from the PDB standards in the input file or from missing or spurious atoms. Please inspect your input file for irregularities and contact us if you need further support.

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ERROR - PDB's with occupancy field equal '1.0'

Submitted by khanhbinh on Sun, 2012-09-23 09:38

I've tried to dock 2 protein in Rosetta dock serve (http://rosettadock.graylab.jhu.edu/) but it always has this problem:

Occupancy Error: Submitted PDB(s) have occupancy field other then '1.0'. Currently we only accept PDB's with occupancy field equal '1.0'. Please fix occupancy field and resubmit the job.

Even when I change all the '0.00' value to '1.00' value. Please check my files to see what happen ?
Thank you very much.

P/S: I change the extension of my file from .pdb to .txt

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Rosetta 3.4 on Ubuntu 12.04 - g++-4.6 not found

Submitted by zoey on Fri, 2012-09-21 07:15

Hi Rosettaers,

I am building Rosetta 3.4 on Unbuntu 12.04 running in VMWare player. I got the following error when I built it with scons bin mode=release:

Running versioning script ... fatal: Not a git repository (or any of the parent directories): .git
Done. (0.1 seconds)
scons: done reading SConscript files.
scons: Building targets ...

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