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What's a good application to thread a sequence over a peptide (of a peptide-protein complex) and minimize?

Submitted by brspurri on Tue, 2013-02-12 08:19

Hi all,

I have a scenario where I have a peptide-protein complex. I would like to thread a series of sequences over the peptide, then minimize the peptide-protein complex. The idea being, I would like to tell which threaded-peptide-sequences would be the "best" binder predictors. Or at least be able to segregate between potential non-binding sequences and binding sequences.

I've been looking at the backrub protocol. Would this be an appropriate application? I don't see immediately how I can thread the sequences over the peptide with this application then.

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ligand conformer generation for enzyme design

Submitted by bo on Mon, 2013-02-11 16:51

Hi everyone,
I'm trying to generate ligand conformers for redesigning an enzyme. I had an input conformation, but when using it to generate conformers, it gave me this error:

Loading internal fraglib
81736 fragments loaded in 0.65 seconds

Title = untitled
Can't assign MMFF type to atom number 44 S
Warning: force field setup failed due to missing parameters for molecule untitled

Can you give me some hints on solving this problem?
Thanks.

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Different Pose Energy Values before and after Dumping

Submitted by oppopomoz on Wed, 2013-02-06 09:35

Im developing a Pyrosetta MC de-novo protein fold prediction method and at the end of the script I 'd want to print the energy values and RMSD from the native structure of my simulations and dump their poses as pdb files. so after doing that i noticed that if I import (pose_from_pdb) these poses and rescore them (using the same energy function I used in the script to score their energies) I get different energy values. Here i list the final part of my script which scores and dumps the poses: print_counter=0 f=open("output.dat","w")

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PyRosetta - Scripts

-loops:refine_repack_cycles option not accepted by loopmodel.linuxgccrelease

Submitted by tsjain on Tue, 2013-02-05 18:47

As per the guide on Kinematic Loop Modeling http://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/df/d..., I am trying to pass -loops:refine_repack_cycles as an option to loopmodel.linuxgccrelease.

However, I get the following error message: ERROR: Option matching -loops:refine_repack_cycles not found in command line top-level context

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comparative modelling and broker

Submitted by felipet on Tue, 2013-02-05 08:33

Hi,

I am trying to perform an abinitio modelling of the full-length structure of a two domains protein, having the crystal structure of the Nterminal one. If I try to use a similar protocol as the demo of comparative modelling with end extension the program stops with the following error:

ERROR: moving_connection.icoor().is_internal() && fixed_connection.icoor().is_internal()
ERROR:: Exit from: src/core/conformation/util.cc line: 100

sometimes the first pdb that comes out is ok, but when it crashes, the position of both domains is strangely far away.

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flexible backbone design (fixbb+relax)

Submitted by sdh_h on Mon, 2013-02-04 03:19

Dear all,

I want to use a two-step design procedure in which a fixed backbone design is combined with a backbone relaxation.
The two steps are supposed to be repeated alternately as long as they bring improvement in the energy.
(something like this http://www.ncbi.nlm.nih.gov/pubmed/22632833)

Which fixbb design parameters are the most important? I use -packing:ex1, -packing:ex2. But perhaps there is something else I should consider?

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symmetric fixbb design with design_hpatch

Submitted by sdh_h on Sat, 2013-02-02 01:48

Dear Rosetta users,

I tried to use hpatch score in symmetric design (-score:weights design_hpatch), but I got this error (rosetta 3.3 and 3.4):

sin_cos_range ERROR: -nan is outside of [-1,+1] sin and cos value legal range

Default and soft_rep_design scores work fine. Also turning off the symmetry (designing just one monomer) makes the error disappear.

Is design_hpatch compatible with symmetric design?

Best wishes,
Staszek

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where is pdb2vall.py

Submitted by tevang on Thu, 2013-01-24 13:35

Where can I find pdb2vall.py script to add extra pdb structures to the fragment libraries? I've searched through Rosetta3.4 bundle, Rosetta3.3_fragments and PyRosetta but couldn't find it.

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nr.fasta

Submitted by silvia on Wed, 2013-01-23 10:08

Hi all,
I downloaded the nr database and I used the formatdb to format the database. Now I have the nr files which have been generated but I have obtained neither the nr.fasta necessary to create the filtnr by using "pfilt", nor the nrfilt files.How can I get them?

Thank you,

Silvia

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