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PDB format for RosettaDNA

Submitted by brspurri on Thu, 2013-05-30 11:21

Hi all,

I am trying to recreate the protocol_capture demo of RosettaScripts/RosettaDNA, but am having some difficulties reading my pdb.
I outputted by starting pdb via PyMol, and on visual inspection of the file everything looks normal. However, when I replace the sample pdb in the RosettaScripts/RosettaDNA directory, I get the output:

```
protocols.dna.util:
Finding basepairs:
There are 0 dna positions:

protocols.dna.util:
Finding basepairs:
There are 0 dna positions:
```

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Rosetta 3 - Applications

Problems with always_constrained_relax_script

Submitted by wsgosal on Wed, 2013-05-29 04:39

I am trying to prepare a structure for Rosetta and trying various flags and methods to relax the structure. One way is to use the "relax_w_allatom_cst" protocol as documented here:

https://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/d9/...

My inputs are...

Case 1. Normal relax

> /Applications/rosetta3.4/rosetta_source/bin/relax.linuxgccrelease -database /Applications/rosetta3.4/rosetta_database/ -ex1 -ex2 -relax:sequence -nstruct 1 -s mypdb.pdb

Case 2. Relax with Constraints

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Rosetta 3 - Applications

ddG filter gives deltaG calculation number?

Submitted by jarod on Tue, 2013-05-28 23:43

Hi,

I used attached "design2.xml" to design interface of Ag-Fab complex (see my previous thread). A "ddG" filter was used in the design script to calculate ddG of mutant.
After the required mutants were dumped out into PDBs, I used another very simple script (attached "ddg.xml") with just only one "ddG" filter to calculate ddG for each output PDB. When I was checking the log file, I found the ddG values calculated by two scripts are different.

For example, for the structure decoy des5xxxx_0005,

its ddG reported in log file of "design2.xml" is about -27:

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Rosetta 3 - Applications

Pepspec Errors running 3.4

Submitted by rrphenix on Tue, 2013-05-28 12:08

I am working on using the application pepspec to identify possible peptides that would bind to a protein of interest but am running into significant difficulties at the actual peptide generation stage.

After running anchordock with three other homologous proteins in order to generate a good estimate of the anchoring residue, I

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Rosetta 3 - Applications

How to generate constraints of active sites from a pdb file of an enzyme

Submitted by Albert on Sun, 2013-05-26 20:07

Greetings, everyone. I got the pdb file of an enzyme, but I don't know how to write the constraints of its active sites.
Could anyone help me solve this problem?
Much appreciate it.

When I open the pdb file with txteditor, I can see coordinates as:
ATOM 1 N HIS A 27 10.218 -30.379 -16.292 1.00 12.31 N
ATOM 2 CA HIS A 27 10.486 -29.045 -15.829 1.00 12.44 C
ATOM 3 C HIS A 27 11.803 -28.537 -16.417 1.00 12.46 C
ATOM 4 O HIS A 27 11.912 -27.351 -16.894 1.00 11.54 O

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Rosetta 3 - General

Rosetta forcefield terms and interpretation

Submitted by zigeuner on Sat, 2013-05-25 16:59

hi, I just spent a bit of time trying to update my rusty knowledge of the reported forcefield terms. I thought I would post the list and see if people can improve on it. I tend to view this as very important info for non-guru users

cheers,

-Louis

fa_atr = full atom attraction
fa_rep = full atom repulsion
fa_sol = full atom solvation via Lazaridis-Karplus solvation model
fa_pair = full atom statistics based pair term, favors salt bridges
hbond_sr_bb = hydrogen short range backbone-backbone
hbond_lr_bb = hydrogen short range backbone-backbone

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Rosetta 3 - General

About align hundreds of pdb structures produced by rosseta membrane abinitio

Submitted by ritacc18 on Wed, 2013-05-22 12:37

Hi,

I have hundreds of pdb structures produced by rosetta membrane abinitio from one sequence.
And I cluster them to get three clusters.
Now I want to align the structures within each clusters, so that I can get RMSD for each cluster.

I used to use MultiProt to align 3D structures, but seems it has a problem dealing with hundreds of structures.

Dose anyone know a better tool (or feature within rosetta, which I'm not aware) to dealing with alignment for many structures?

Thanks for your help!
Rita

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Rosetta 3 - General

No interface for protein - Interface Analyzer

Submitted by aloshbau on Tue, 2013-05-21 21:00

I'm trying to run interfaceanalyzer on a PDB with two chains (A and B). I first tried using the -fixedchains flag to specify the two separate chains for determining the interface, but get the following error:

~/Applications/rosetta3.4/rosetta_source/build/src/release/macos/10.7/64/x86/gcc/4.2/InterfaceAnalyzer.default.macosgccrelease -database ~/Applications/rosetta3.4/rosetta_database/ -l list3 -tracer_data_print false -out:file:score_only score.sc -pack_separated true -add_regular_scores_to_scorefile true -fixedchains A -pose_metrics::inter_group_neighbors_calculator 3

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