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packing option "explicit_h2o" and "solvate"

Submitted by SunH on Wed, 2010-11-17 00:03

Hi everyone,
Does anyone know whether the packing option "packing::explicit_h2o" and "packing::solvate" work out in Rosetta3.1?
This paper "A 'Solvated Rotamer' Approach to Modeling Water-Mediated Hydrogen Bonds at Protein–Protein Interfaces" said that Rosetta could recover water-mediated h-bond using a rotamer library called Solvated Rotamer. How to use it, add "explicit_h2o" or "solvate" flag ? But I read the code of Rosetta3.1 and couldn't find the source code implemented these two option.

Thanks!

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Abinitio Calculations - typical parameters

Submitted by vamsi on Thu, 2010-11-11 07:06

Dear all,
I am using rosetta for abintio calculations for a while now. I am curious to know what are other parameter other than mentioned in the documentation, to play with to simulate protein size of 150 aminoacids. I am not really satisfied with the results obtained with typical parameters and wondering my laptop took only like one hour to complete the job ( but heard previously it is computationally intensive process)

Here is my flag file
-database /home/vamsi/Programs/Rosetta31/rosetta_database/
-abinitio
-in:file:fasta inputs/t000_.fasta

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Rosetta 3 - General

relax with restraints

Submitted by jtmacd on Mon, 2010-11-08 09:11

Hi there,

Is it possible to use the relax app to relax an structure while restraining the C-alpha coordinates to their initial positions in order to stop things blowing up? There seems to be an option -constrain_relax_to_start_coords but it doesn't appear to have much effect when I tried using it.

thanks for your help!

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Does Rosetta have homology modeling protocol?

Submitted by SunH on Thu, 2010-11-04 07:36

Hi all,

Does Rosetta have a homology modeling protocol like SWISS-MODEL or MODELLER? I couldn't find it in source code.
I want to predict the structure of a sequence and then do a protein-protein docking, need I use MODELLER to create the structure from sequence and template pdb before repacking or loop modeling using Rosetta?

Thanks.

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