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high resolution protein docking doesn't work

Submitted by albumns on Thu, 2010-12-02 02:36

Hi
I am using rosetta docking_protocol.linuxiccrelease @flags > docking.log for initial protein docking. 10000 initial pose(only backbone) were generated by this. Then I clustered top200 pose by cluster.linuxiccrelease @flags >& cluster.log &
The best scoring one from the largest cluster were submitted for rosetta refinement(add sidechain and hydrogens) :relax.linuxgccrelease @flags > log

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Rosetta 3 - General

question about protein docking results

Submitted by albumns on Thu, 2010-11-25 08:19

Hi
I am using the docking_protocol.linux for high resolution complex. I found there are many parameters in *.fasc file such as:

fa_atr fa_dun fa_rep fa_sol hack_elec hbond_bb_sc hbond_lr_bb hbond_sc hbond_sr_bb interchain_contact interchain_env interchain_pair interchain_vdw.

So, I am wondering which one would be a measurement for final model selection?

BTW, could this protocol support MPI multiple CPU running?

THX

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Rosetta 3 - General

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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