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PDB file name too long to be handled by file system

Submitted by dave on Thu, 2019-08-08 03:10
Category: 
Structure prediction

Hello,

in ddg_monomer module, we have encountered a problem with the length of the PDB file name when predicting mutant with 50+ mutations. Since Rosetta constructs the PDB file name based on the mutations included in the predicted mutant as prefix + list of mutations, with a large number of mutations this file name can be longer than 255 characters which causes the file system to be unable to store the PDB file. Is there any way how to prevent this behavior, for example set rosetta to store PDB file under user given name? Thank you for you answer.

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Rosetta 3 - Applications

Where to find old version of Rosetta with git version number

Submitted by mao_x on Wed, 2019-08-07 01:22
Category: 
Compilation

Hi, there:
    I am reading some papers using Rosetta for modeling work. In the papers, they mentioned rosetta git version number. I am just wondering  if anyone can tell me where I can find some old version of rosetta according to git version number. Thank you very much for your help.

 

Best,

Mao

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Rosetta 3 - General

bin folder does not appear after compiling

Submitted by kalechips on Tue, 2019-08-06 06:50
Category: 
Compilation

Hello, 

I've previously never had trouble downloading Rosetta (I've done it twice successfully before) until now.

I'm trying to install Rosetta on Linux 3.1. When I go to Rosetta/main/source and type in ./scons.py -j3 mode=release bin it doesn't ever throw an error, but the bin file does not appear. 

Does anyone know how I can fix this?

Thank you

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Rosetta 3 - Build/Install

InterfaceAnalyzer：“too many tries in fill_missing_atoms!”

Submitted by mxp on Tue, 2019-08-06 00:41
Category: 
Scoring

Hey Guys,

We are trying to use  "InterfaceAnalyzer"  to  analyze a  PDB,  then we get this:

......

.....

core.conformation.Conformation: [ WARNING ] missing heavyatom: C7 on residue pdb_HSD 152
core.conformation.Conformation: [ WARNING ] missing heavyatom: O4 on residue pdb_HSD 152
Error: [ ERROR ] ERROR: Exception caught by JobDistributor while trying to get pose from job 'complex_0_0001'
Error: [ ERROR ] 

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Rosetta 3 - Applications

Design with non-canonical amino acids (NCAA)

Submitted by yinasun on Mon, 2019-08-05 00:34
Category: 
Non-Canonical Peptides

Hello everyone, I would like to ask, how to add the following lines when creating a parameter in the rosetta for a non-standard amino acid containing a methyl group on the backbone? M ROOT 13 M POLY_N_BB 13 M POLY_CA_BB 14 M POLY_C_BB 15 M POLY_O_BB 16 M POLY_IGNORE 2 3 4 5 6 8 9 10 11 12 M POLY_UPPER 7 M POLY_LOWER 1 M POLY_CHG 1 M POLY_PROPERTIES PROTEIN POLAR CHARGED M END

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Rosetta 3 - General

Rosetta job distribution error

Submitted by ss on Thu, 2019-08-01 09:26
Category: 
Design

Hi There,

 I am following rosetta protein design but every time I am getting job distribtion error message.  Here is output

 

<ROSETTASCRIPTS>

    <SCOREFXNS>
        <talaris_full weights=talaris2014>
            <Reweight scoretype="coordinate_constraint" weight=0.4/>
            <Reweight scoretype="res_type_constraint" weight=0.4/>
        </talaris_full>

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Rosetta 3 - General

Unable to create col_complex.pdb file

Submitted by sayan500 on Tue, 2019-07-30 22:08
Category: 
Docking

I am new to Rosetta and was trying Protein-Protein Docking tutorial. I was about to run a local docking but it gives me an error saying that 

"ERROR: Cannot open file "input_files/col_complex.pdb"

so when I checked the "flag_local_docking" file there is a file called col_complex.pdb needed as input. But I don't understand how to build this file.

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Rosetta 3 - General

MakeRotLib

Submitted by yinasun on Sun, 2019-07-28 20:08
Category: 
Non-Canonical Peptides

How do I use the rotamers of natural amino acids instead of non-standard amino acids when designing non-standard amino acids?

because I see "The ROTAMER_AA params file line allows you to skip the MakeRotLib step if you want to let your tyrosine related NCAA use tyrosine rotamers"

for example，Non-standard amino acids pTyr is instead of Tyr, IWhat parameters should I add in pTyr.params?

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Rosetta 3 - General

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