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PIKAA in resfile does not mutate Cys in disulfide bond to specified residue

Submitted by attesor on Fri, 2014-03-14 07:53
Category: 
Design

Hi, I used fixbb in Rosetta 3.4 to thread a sequence on a template structure. There is a disulfide bond in the template structure, say, between two residues Nr. 20 and 50. My resfile looks like this: NATAA # keep native aa but packable! ... 20 A PIKAA G ... 50 A PIKAA G ... However, in the threaded model, all mutations specified in the resfile were realized except the two cystine residues. How can I force fixbb to mutate the two cystine residues?

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Rosetta 3 - Applications

smoothly kill a mpirun process

Submitted by fred on Tue, 2014-02-18 06:06

Hi there,
Sorry about this, perhaps, off topic question. The problem is I´m running a MPIRUN loop modelling processes, which I've asked for 500k decoys. Well, i've changed my mind and decided to stop it before end. I'm afraid, however, that an abrupt interruption will damage my big silent file. So, is there any way to smoothly kill such a process?
Thanks in advance.

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Rosetta 3 - General

Interface energy vs binding energy

Submitted by Apiwat on Wed, 2014-02-05 00:47

Hi all,

I know, there is a little bit difference between interface energy and binding energy in protein docking.
Interface energy come from, separate 2 chain (same pose) far away and then calculate total energy
Interface energy= (complex total energy) - (separated total energy)

Binding energy com from , calculate total score for each individual chain (different pose)
Binding energy = (complex total energy) - [ (individual chain 1 total energy) + (individual chain 2 total energy) ]

right ?

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Rosetta 3 - General

rosetta_2013wk52: make_fragments.pl failed

Submitted by fred on Thu, 2014-01-30 12:41

Hi there,
Here goes a cut&paste of the rosetta_2013wk52 make_fragments.pl output.
This is a kind of low priority since Rosetta-3.5 make_fragments is running just fine.
Also, I could not be able to complete fragment_picker with the extra option boost.
Best

###############
cmd is: /home3/cluster/apps/fred/rosetta_2013wk52/tools/fragment_tools/psipred/bin/psipass2 /home3/cluster/apps/fred/rosetta_2013wk52/tools/fragment_tools/psipred/data/weights_p2.dat 1 1.0 1.0 psipred_ss2 psipred_ss > psipred_horiz
psipred file ok.

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Rosetta 3 - Applications

make_fragments.pl can't find ForkManager.pm

Submitted by fred on Wed, 2014-01-29 07:42

Hi there,
How can modify make_fragments.pl script so as it finds the necessary Perl modules?

-bash-4.1$ ./make_fragments.pl
Can't locate Parallel/ForkManager.pm in @INC (@INC contains: /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at ./make_fragments.pl line 1840.
BEGIN failed--compilation aborted at ./make_fragments.pl line 1840.
-bash-4.1$ locate ForkManager.pm

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Rosetta 3 - Build/Install

Cannot get a negative score after relax

Submitted by kxiao on Tue, 2014-01-28 22:28

Dear rosetta_users,
I am trying to relax a subunit of a actin filament(PDB ID: 3g37, chain O).
I have deleted all the modification and ligands, generated side-chains atoms by using MaxSprout, and add missing atoms by DeepView. Then I tried to use the relax function of rosetta before next step, with constraint. However, the total score of the structure is ~1200, which seems unreasonable. I also got OPT-H WARNING about chi angle, so I wonder if the high score is related with these warnings. What can I do to get a negative, at least much lower score of the structure?

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Rosetta 3 - Applications

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