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Approximating CHARMM energy by the rosetta scoring function

Submitted by ajasja on Fri, 2014-06-20 02:16
Category: 
Scoring
PyRosetta

Is it possible to approxmate the CHARMM energy (function) by the rosetta scoring function?

As a starting point I could work with fixed angles and bond lengths, so I guess setting the weghts for fa_atr, fa_rep and fa_elec to 1 and all the rest to zero is a good start. But is it possible to somehow load the CHARMM diheral parameters?

Thank you for your help,
Ajasja Ljubetič

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PyRosetta - General

Fastrelax problem

Submitted by Pernille on Fri, 2014-06-20 00:16
Category: 
Docking

Hi all
I am docking several different proteins and before docking I use fastrelax to relax the individual proteins.
Fir some of the proteins (they are all less than 200 aa) Fastrelax takes extreemly long to generate 25 poses.
For one in particular following error pops up:

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Rosetta 3 - Applications

Cluster decoys after running PlexPepDock

Submitted by phanvy on Thu, 2014-06-19 06:03
Category: 
Docking

Hello everone

After running the Plexpepdock, I have 40000 decoys. I try to use the cluter program of Rosetta 3.4 . But, I do not understand the meaning of cluster. Because , after I tried to run with 200 decoys and get the out:file with 200 file c.0.XXX.pdb format. I do not understand how cluster work.

Flags:
-in:file:silent decoys.silent
-database /home/tuongvy/SW/rosetta3.4/rosetta_database
-in:file:fullatom
-score:weights
-score:patch
-cluster:sort_groups_by_energy

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Rosetta 3 - General

Error runining PyRosetta "undefined symbol: __sinh_finite"

Submitted by ajasja on Wed, 2014-06-18 08:09
Category: 
PyRosetta

Hi all!
*OS*: Mint Linux 17,
64bit Linux (3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:11:08 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
*Python*: Python 2.7.7 |Continuum Analytics, Inc.| (default, Jun 2 2014, 12:34:02) [GCC 4.1.2 20080704 (Red Hat 4.1.2-54)] on linux2
*PyRosseta*: PyRosetta.Ubuntu-12.04LTS.64Bit.devel-r56795

While trying to import PyRosseta I get the following error:
"ImportError: rosetta/libmini.so: undefined symbol: __sinh_finite"

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PyRosetta - Build/Install

MPI nodes hanging and output log incomplete

Submitted by yuvals on Wed, 2014-06-18 05:40
Category: 
Scoring

I'm using MPI with the PeptideDeriver pilot app (which I reworked to support JD2). I am running into some problems:

1. nodes that have finished jobs stall with 100% cpu usage while the entire MPI run isn't complete.
2. some tracer.log files don't contain all of the output -- for instance, the master node might have gotten a success message from a node, but not all the output of that job appear in the tracer.log file (the last bit is missing)
3. some jobs aren't finishing.

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Rosetta 3 - General

Ambiguous constraints are ignored in ab initio

Submitted by mschneid on Wed, 2014-06-18 04:33
Category: 
Structure prediction

Dear Rosetta Commons,

I recently wanted to use a set of ambiguous constraints in structure prediction and I prepared a file that looks like this:

AmbiguousConstraint
AtomPair CB 26 CB 38 BOUNDED 1.5 8.0 1.5 NOE
AtomPair CB 28 CB 61 BOUNDED 1.5 8.0 1.5 NOE
AtomPair CB 26 CB 61 BOUNDED 1.5 8.0 1.5 NOE
END_AMBIGUOUS

Unfortunately, it seems that the ab initio application is ignoring the ambiguous constraints. No constraints are used in the prediction and also there is not constraint score term in the final score file.

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Rosetta 3 - General

Fastrelax problem

Submitted by Pernille on Tue, 2014-06-17 08:59
Category: 
Docking

Hi all
I am docking several different proteins and before docking I use fastrelax to relax the individual proteins.
Fir some of the proteins (they are all less than 200 aa) Fastrelax takes extreemly long to generate 25 poses.
For one in particular following error pops up:

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Forums: 
Rosetta 3 - Applications

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