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Error when trying to use xml script to design PDB

Submitted by Wexter300 on Fri, 2023-02-24 13:29
Category: 
Design

I am trying to mutate and relax the 7ah0 pdb using the following xml script:

<ROSETTASCRIPTS>

<SCOREFXNS>

<ScoreFunction name="sfxn" weights="ref2015"/>

</SCOREFXNS>

<RESIDUE_SELECTORS>

<Index name="res1" resnums="388A"/>

<Index name="res2" resnums="389A"/>

<Index name="res3" resnums="390A"/>

<Index name="res4" resnums="391A"/>

<Index name="res5" resnums="392A"/>

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Rosetta 3 - General

Rosetta remodelling - how to change the added residue type instead of just VAL

Submitted by xuezhi on Wed, 2023-02-15 14:00
Category: 
Design

Dear sir,

I am new to Rosetta. I followed the rosetta protocol to pad a few residues to N, C terminals of my protein. I follow the remodel.static.linuxgccrelease instructions. Created pad.bd as below. Then I run "rosetta_bin_linux_2021.16.61629_bundle/main/source/bin/remodel.static.linuxgccrelease -in:file:s 1mhp_H_0001.pdb -remodel:blueprint 1mhp_padpadded   -remodel:dr_cycles 1 -num_trajectory 1 -save_top 1" . but it only added Val reisidues. I want to added non-specified residues but not all into VAL. how to fix this? Kind regards.

 

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Rosetta 3 - General

Truncating a protein using rosetta

Submitted by Wexter300 on Mon, 2023-02-13 12:05
Category: 
Design

I am a beginner to rosetta, and I was wondering if there is a way to truncate/ get rid of a specific part of a sequence and create a stable protein? I have the PDB of the protein and the specific parts of the sequence I need to truncate. It is to get rid of loops at the terminus. Do I just input a sequence to rosetta with the unwanted parts deleted and have it model the protein ?

Sequence : 

G-SPELREKHRALAEQVYATGQEMLELREKHRALAEQVYATGQEMLKN-TSN

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Rosetta 3 - General

How to add uncommon metal elements into Rosetta and make it recognizable?

Submitted by JasonIsaac on Thu, 2023-02-09 00:08
Category: 
Design

HI everyone, I want to RosettaMatch to introduce a ligand into a scaffold protein, but the ligand contains uncommon metals like Rh, I am afraid Rh is not recognizable like Fe by Rosetta. 

So I want to ask about how to add a new metal element to Rosetta, and how many files should I edit to make sure it's done? As far as I know, maybe I have to edit atom_type_sets and residue_types sets under database/chemical/, but more specifically, I have no idea.

Any suggestions would help!  And thanks for you time and effort.

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Rosetta 3 - General

Error in rosetta_scripts.mpi.linuxgccrelease: double free or corruption (!prev): 0x0000000007697a90

Submitted by almeida85 on Thu, 2022-11-17 01:04
Category: 
Design

Hello,

I am running  a xml script with rosetta_scripts (Rosetta 3.14, v2022.11) in my HPC cluster and I am getting the following error:

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Forums: 
Rosetta 3 - General

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