You are here

Home

Unsolved

The problem hasn't been solved

total energy score of the pdb structure

Submitted by Lindsay on Tue, 2012-05-01 12:14

Dear ALL,
I run the score_jd2 program to calculate the total energy of the pdb structure.
score_jd2.linuxgccrelease -database rosetta_database/ -s 1xnz.1.A.2.A_0001.pdb
and get a file named score.sc
SCORE: -249.622 -1098.702 251.556 555.107 2.612 11.728 -24.622 -55.572 -81.320 -24.066 -15.083 0.000 0.000 0.000 0.000 -4.476 3.227 294.517 -24.189 -40.340 0.000 0.000 0.000 1xnz.1.A.2.A_0001_0001

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

tyrosine structure error

Submitted by dave on Mon, 2012-04-30 04:38

Hello,
I am using Rosetta 3.3 and I have a problem with matching. In my cstfile I want to model a H-bond using the atom_type: Hpol of several residues. Results from Matcher are completely wrong in the case of Tyr. Hpol atom is not located on the phenolic oxygen but on the CD1 atom of Tyr which is now double protonated. I was looking into ~/rosetta3.3/database/chemical/residue_type_sets/fa_standard/residue_types/l-caa but Tyr is here defined correctly. I tried to delete and create Dunbrack02.lib.bin once again but no change was observed.

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

How to optimize the orientations of polar hydrogens in PyRosetta

Submitted by xfliu on Sat, 2012-04-28 16:33

Hi,

I wonder if there is a way to trigger the optimization of polar hydrogens in PyRosetta just like the "-no_optH" option in Rosetta when reading structure information from PDB files into Pose. Because I found many potential hydrogen bonds in the original PDB structures were interrupted by the wrongly added hydrogens by default which result very high energy scores.

I have not found any routines to set free the movemenet of hydrogens in the MoveMap settings.

Post Situation: 
Unsolved
Forums: 
PyRosetta - General

Problem with clustering 1000 centroid pdbs

Submitted by doranhen on Sat, 2012-04-28 10:34

Hi,
I am trying to use rosetta3.1 cluster function to cluster 1000 pdbs of a homodimer that were created by Symmdock of rosetta3.2 and are still in centroid mode. Even if I get the pdb outputs for the clusters , I still get an output txt file that crashes at line 2,707,992 and doesn't give me the clustering information. The problem is that there are so many warning messages of the following types for each atom:
core.conformation.Conformation: [ WARNING ] missing heavyatom...
core.io.pdb.file_data: [ WARNING ] can't find atom for res 84 atom CEN...

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

double mutations scan

Submitted by Lindsay on Fri, 2012-04-27 12:51

Dear ALL,
I try to scan all the possible double mutations use this command"~/rosettabin/pmut_scan_parallel.macosgccrelease -database ~/rosettadb -s 1ABC.pdb.gz -double_mutant_scan -output_mutant_structures -ex1 -ex2 -extrachi_cutoff 1 -use_input_sc
-ignore_unrecognized_res -no_his_his_pairE -multi_cool_annealer 10 -mute basic core".
But I also want to fix all the residues as NATRO except the mutated residues. What command should I use? Thank you!

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Picking the correct model from a large set of decoys (30,000+)

Submitted by brspurri on Thu, 2012-04-26 15:37

Hi everybody,

I'm been fairly successful at creating a large list of decoys for several of my project (de novo, loop modeling, etc). My runs typically produce 30,000 to 50,000 decoy structures, which I am under the impression is a decent number.

What is the best method to determining the "most accurate" structure from these decoys? Do I cluster first, take the lowest energy (c.0.0.pdb). Or do I look at the top scoring structures from each cluster? (c.0.0.pdb, c.1.0.pdb, etc). Or do I score the entire set and take the lowest scoring structure to be the most accurate, without clustering?

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Pages

Subscribe to RSS - Unsolved