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libdevel not found while running Rosetta using mpi

Submitted by priyaps on Thu, 2013-08-08 09:28

Hello Rosetta experts,
I am very new to Rosetta and am trying to compile Rosetta3.4 (tried even Rosetta3.5) on a linux cluster with the following command:
./scons.py bin mode=release extras=mpi -j 12
The installation appears to have finished fine though when I try to run a job using mpirun it gives me the following error:
error while loading shared libraries: libdevel.so: cannot open shared object file: No such file or directory.
From this thread, it appears to me that Rosetta should not ask for libdevel.so library.

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Rosetta 3 - Build/Install

opt-E Reference energies

Submitted by vijayan on Wed, 2013-08-07 07:35

Hi all

Going through the paper by Elizabeth Kellog et al in Proteins, i realized that the standard reference energies are not well optimized for Delta-deltaG calculation but more suited for sequence recovery. However, it is stated that a new set of opt-E weights yields better correlation. Can any one help me out in figuring where these new set of reference weights exists and how to incorporate them in the standard score12 function.

Thanks in advance

Regards,
Vijayan.R

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Rosetta 3 - General

RosettaVIP

Submitted by nick.polizzi on Tue, 2013-08-06 15:13

Hi, I'm hoping there might be a quick way to alter the VIP code so that it reads res and cst files. This thread seems to tackle the cst file problem: https://www.rosettacommons.org/node/3268 (although I admit I haven't tried it yet to see if it works...), but not necessarily the resfile problem. I'd essentially like for VIP to redesign with a more restricted APOLAR set, by excluding W and Y. Any ideas? Thanks!!

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Rosetta 3 - General

Alanine Scanning

Submitted by gjbartlett on Mon, 2013-08-05 07:02

Hello,

I'm trying to run alanine scanning on a structure using the RosettaScripts program. I've used the attached xml input, gleaned from looking through the forums for alanine scanning, with the following command-line:

/bin/rosetta_scripts.linuxgccrelease -s 2K2I.pdb.clean -use_input_sc -nstruct 1 -jd2:ntrials 1 -database rosetta_database/ -ex1 -ex2 -parser:protocol ala_scan.xml -out:file:2K2I.pdb.clean.out -out:file:scorefile 2K2I.pdb.clean.sc

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Rosetta 3 - Applications

How to sort a Silent File based on RMSD

Submitted by JadAbbass on Sun, 2013-08-04 14:40

Dear all,

I have a silent file of 20,000 structures with associated rms for each one. The typical cluster application in Rosetta is not very useful as it clusters them based on energy score.

1. Simply, I want to sort the structures based on the value of rms from the lowest (best) to the highest (worst), how to do so?

2. Is there any way to calculate the average of the rms of all decoys?

Thank you for your time and effort,

Jad

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Rosetta 3 - Applications

Multi Ligand docking to a protein

Submitted by Vaish86 on Sun, 2013-08-04 10:46

Hi! I am new to PyRosetta and from Pure Life Science background.
I am trying to dock three ligands to a protein and I have gotten as far getting the my protein with concatenated ligand pdbs to be accepted as pose. I am having a block as to what I should do next.
Should I be following DockingProtocol() or is there any other set protocol?

I would appreciate any help in the right direction.

Thanks
Vaishnavi

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PyRosetta - Scripts

Ligand creation

Submitted by Prasanth Kumar on Fri, 2013-08-02 09:48

Hi guys,
I have some ligand structures in paper(overall structure). I want to convert those paper structure into pdb.(I have details about the bond order and bond distances).

So can someone can suggest me which is the best open source software to do this (I want to use generated ligand in liganddock application)

Thank in Advance
- K.Prasanth

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Rosetta 3 - Applications

Rosetta Holes and Packstat scoring

Submitted by nick.polizzi on Fri, 2013-08-02 09:06

Hi, I'm trying to use rosetta holes to design a well packed 4-helix bundle around a Zn porphyrin. I'd like to use the hole_min energy weight to bias the design toward a well packed structure. It seems I want to increase the cavity probe radius, since holes does not seem to penalize the structures for very widely separated helices (i.e., a water molecule can definitely get in between the helices, so holes doesn't seem to penalize this, but I'd like it to.) So I'd like to increase the probe radius, and have holes (or packstat) rescore the structure accordingly.

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Rosetta 3 - General

Energy Minimization

Submitted by bharat_46010 on Wed, 2013-07-31 20:45

Hi,

I searched for a basic protocol that can be used to minimize my four residue turn structure and I didn't find any. Therefore, I used the following method :-

scorefxn = create_score_function_ws_patch("standard","score12")
mm = MoveMap()
mm.set_bb(True)
pose_move_map.set_chi(True) ## For side chain minimization
mm.set_bb_true_range(1,4) ## Here range means 1 to 4 or the minimzation is applied only to residues 1 and4 ??

minmover = MinMover(mm, scorefxn, 'dfpmin', 10, True) ## I don't know the meaning of dfpmin,10,True. I saw it somewhere and used it

minmover.apply(pose)

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