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How do I add hydrogen atoms to my PDB file?

Submitted by monos_morpheus on Wed, 2011-03-30 03:30

I'm currently using Rosetta 3.2.1, and I wish to add missing H atoms to my PDB file. I know that in the past, a clean_pdb.py script was created by the Meiler Lab to help with such a problem. However, I'm unable to locate this file anywhere in Rosetta 3.2.1. Is there any ways to locate this file or is there other scripts made to satisfy such a problem.?

Thanks.

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Rosetta 3 - General

Why a paralleled Rosetta perform like a normal one?

Submitted by ice_flame on Mon, 2011-03-28 22:23

Hi all,

I newly built a paralleled Rosetta2.3.0 with OpenMPI 1.4.3. I used "make mpilam" to build it.
After building, I tested it with the following command:

mpirun -np 16 /home/knight/softwares/Rosetta-2.3.0/rosetta++/bin/rosetta.mpilam -mpi_task_distribution -s 1ubq.pdb -design -fixbb -resfile resfile -ex1 -pdbout test -ndruns 2000 > 1ubq_fixbb_mine.log

-np = 16 since I have 16 cores.

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Rosetta++ - General

Help with get_pdb.py for PDB file cleaning

Submitted by lzx32 on Mon, 2011-03-28 02:11

Hi, I am following the suggestion from one of the posts here to use get_pdb.py to clean up my PDB files. However, I always got the error message:

Traceback (most recent call last):
File "/usr/local/rosetta3.2/rosetta_source/src/python/apps/public/get_pdb.py", line 69, in ?
assert( len(argv)>2)
AssertionError

Did I do something incorrectly? Thanks in advance for any kind help!

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Rosetta 3 - General

help with perturbation docking please

Submitted by einew on Fri, 2011-03-25 16:16

We ran a centroid blind docking for a published reference system. [Its docking had been calculated with BiGGER - don't know if this is relevant]. We ran 1000 structures. Among the 5 most negative scores was a structure that looked as if it could be perturbed into one that resembles the structure in the literature. We ran full atom perturbation docking with an angle of 45 deg & a 10A distance.

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Rosetta 3 - General

abintio clustering - funnel plot

Submitted by vamsi on Fri, 2011-03-25 09:18

Hi,

i have run abintio structure prediction and produced nearly 20.000 structure. please help me how to cluster these structures and how to create funnel plot to select native like structure from silent file. Do u think 20,000 structures is good enough to predict native struture of 146 residues. Is there any way to filter strutures using secondary structure prediction during clustering stage. I know rosetta 3.2 supporting SS based filtering but i have all my predictions with rosetta 3.1.

Thank you in advance for all your help

with regards,
vamsi

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Rosetta 3 - General

error mesages from RosettaDock

Submitted by AlanZhao on Mon, 2011-03-21 11:42

I am using RosettaDock (from Rosetta 3.1 package) to generate some predicted protein complexes. I got some errors during a few cases in my dataset.

It says
"ERROR: f.check_fold_tree()
ERROR:: Exit from: src/protocols/docking/DockingProtocol.cc line: 327".

I also attached a log file of one of these error cases.

Could some one help me to solve this problem? Thanks a lot.

Alan

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Rosetta 3 - Applications

low resolution blind protein-protein docking with a ligand

Submitted by einew on Sun, 2011-03-20 13:59

We're trying to repeat published docking results with Cytochrome C & Human neuroglobin, because we want to compare that to docking a different globin to Cyt C. Low resolution blind docking of the protein only [no heme groups] produces 1000 structures 2-3 days on the linux station we're using. However, the interface region in the published structure includes the space in which the hemes sit, so we think including the hemes will be more accurate. With the help of kind people on this forum, we were able to get to the requisite params files & docking partner syntax.

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Rosetta 3 - General

Structure prediction based on template -> Documentation comparative modeling of protein structures

Submitted by maxebert on Sun, 2011-03-20 01:15

Dear Forum,

I am playing around with Rosetta since 2 days now but I still can't get a good output. So here is what I am doing. First to proof the efficiency I try to predict the structure of an amino acid sequence from which the crystal structure is already determined by using this command:

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Rosetta 3 - General

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