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PyRosetta - General

Model two domain protein

Submitted by sn on Sat, 2017-05-06 13:21

Category:

Design

Hi,

I want to model a protein that has two domains. I have two separate domains modeled using Rosetta. I want to merge these two domains based on the cst file that gives inter domain distance constraints.

What are some of the best ways to model it? These domains are asymmetric. Can I use RosettaCM to do the modeling? Or should it be more like fold and dock?

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optimisation of a protein-protein interface

Submitted by sdh_h on Thu, 2017-05-04 05:06

Category:

Design

Scoring

Symmetry

Dear Rosetta users,

I have a symmetrical homo-dimeric structure for which I would like to select a single point mutation that will increase the affinity between the monomers. I thought about design&relax protocol, in which one position is designed while the remaining ones are only allowed to repack. Such a protocol would be used to scan all the interface positions.

My questions is how to set up this in Rosetta Scripts? Perhaps there are easier/better ways to do this?

Thanks for help! Staszek

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Including waters in RosettaCM

Submitted by ajkal on Thu, 2017-04-27 11:59

Category:

Structure prediction

I want to include several binding site waters in my homology model, since they seem to have an important impact on the configuration of the cofactor (GTP & Mg2+). I.e. when I do the homology model without the waters, the position of the cofactor is significantly different from the crystal structure template, despite the surrounding residues being completely conserved. The cofactor occupies a space that is normally occupied by several structurally conserved water molecules. However, when I try to include the waters I get the error message:

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Adding centroid .params files for non-canonical residues based on all-atom .params files

Submitted by jcminerlanl on Thu, 2017-04-27 09:28

Category:

Loop Modeling

On the matter of using GenKIC to model a loop of noncanonical groups like beta-peptides or peptoids, the GenKIC program falters due to lack of centroid data.

The requirements for centroids is confirmed by removal of the ALA.params file from: database/chemical/residue_type_sets/centroid/residue_types

This causes the same error as it does for sequences of beta-peptides and peptoids for which there are all-atom params files in: database/chemical/residue_type_sets/fa_standard/residue_types/

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weights for pH_protocol

Submitted by fmerino on Wed, 2017-04-26 07:14

Category:

ROSIE

Dear all,

I have been recently testing pH_protocol to calculate the pKa of one of my proteins. In the original paper, the authors include the weights function to be used with the protocol:

fa_atr 0.8

fa_rep 0.44

fa_sol 0.65

fa_intra_rep 0.004

fa_dun 0.56

hbond_lr_bb 1.17

hbond_sr_bb 1.17

hbond_bb_sc 1.17

hbond_sc 1.1

hack_elec 1.0

e_pH 1.0

ref 1.0

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rosetta compile

Submitted by MA on Wed, 2017-04-26 00:46

Category:

Compilation

Hi, I am beginner using rosetta, I used Scons to compile rosetta code and it is successful. I used Anjuta(IDE) to compile AbinitioRelax.cc and generated an AbinitioRelax.o file,when i used g++ to Compile it into executable file, it return the wrong information, as follows:

root@ma:/home/ma/rosetta/main/source/src/apps/public# g++ AbinitioRelax.o

AbinitioRelax.o: In function `main':

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New CSRosetta toolbox

Submitted by sn on Mon, 2017-04-24 12:42

Category:

Structure prediction

Hi,

I am working for one of the labs, I have been making changes to CSRosetta toolbox like making it compatible with latest versions of Rosetta and would like our lab dir be added into the commons repo. I did not know who to contact. I can give more details about the lab, changes and so on.

Thanks.

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Fast relax not working

Submitted by eyong123 on Fri, 2017-04-21 06:06

Category:

Design

Hi I have not used Rosetta for a while. i wanted to relax my receptor for enzyme design and i kept on having the message

Evaluation Creator active ...

protocols.relax.FastRelax: WARNING: Pose has no residues. Doing a FastRelax would be pointless. Skipping.

protocols.jd2.JobDistributor: S_0001 reported success in 0 seconds

protocols.jd2.JobDistributor: no more batches to process...

protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs att

here is my flag file

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Is there a way to calculate chi1 and chi1+chi differences between two structures?

Submitted by sn on Thu, 2017-04-20 21:46

Category:

Structure prediction

Hi,

I looked up some of the options for various protocols to see if there is a way to calculate chi1 and chi1+chi2 measures for two structures. Essentially I want to compare the xray with that of the model predicted by Rosetta.

Thanks.

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