Random perturbations to peptide backbone
Submitted by Martin Floor on Mon, 2018-12-10 17:16
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Regarding snugdock Ag-Ab score
Submitted by ss on Mon, 2018-12-10 14:47
Category:
Docking
Hi There,
I am running snugdock locally for an Ag-Ab complex. Program is running fine but I am getting all score value 0.00.
SCORE: total_score rms CAPRI_rank Fnat I_sc Irms Irms_leg atom_pair_constraint cbeta cen_rms chainbreak complex_normalized dG_cross dG_cross/dSASAx100 dG_separated dG_separated/dSASAx100 dSASA_hphobic dSASA
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ddG calculations to study point mutations
Submitted by N.Chopra on Fri, 2018-12-07 12:36
Category:
Scoring
Hi,
I am using Rosetta protocol to determine ddG changes on point mutations in a peptide bound to a protein complex. I first used FastRelax to remove any steric clashes in the protein structure and then ran the ddG protocol to generate ~1000 structures till there is no change in ddG values. I now want to build a correlation plot between the Rosetta ddG values and experimental calculations.
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Threading with Ligand
Submitted by ekwan on Thu, 2018-12-06 15:10
Category:
Structure prediction
Hi everyone,
I'm trying to use the partial_thread application to fill in some gaps in a PDB crystal structure, 2hko. This structure has an FAD ligand and a key water I'm trying to keep during threading. I've cleaned the file as recommended, changed the FAD ligand atom types to match the canonical Rosetta atom types, and made similar changes to my water. While the threading runs, the ligand gets thrown out.
This is the command I used:
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Weighted scores??
Submitted by sizhang on Wed, 2018-12-05 15:22
Category:
Structure prediction
Hi all,
Recently, I used the one point mutation on Rosetta Backrub server for getting predicts of mutation. What I got are weighted scores after calculations.
My questions are 1.) what's the units of these weighted scores?
2.) what's the relationship between weighted scores and delta delta G (delta G of mutation - delta G of wild type)?
3.) In the output file, these weighted scores (total) are positive for both wild type and mutation. Are they correct?
I'll appreciate for any help from you.
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docking parse error
Submitted by dave on Tue, 2018-12-04 08:41
Category:
Docking
Hello,
I'm trying to use the highres docking protocol with rosetta3.9 and I still get this error (see below), no matter what I do with the xml protocol (attached):
I would appreciate any suggestion
best regards,
Dave
The command I run:
rosetta_scripts.static.linuxgccrelease -in:file::s 1mj5.pdb -parser:protocol docking.xml -extra_res_fa r_lig.params
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SnugDock - What protocol should I use?
Submitted by dfcoelho on Tue, 2018-11-27 07:32
perturb_temp flag
Submitted by Loki01 on Tue, 2018-11-27 05:06
Category:
Loop Modeling
Dear all,
I am trying to understand this flag better. I believe the default temperature for Monte Carlo is 0.8 but I cant find out what does that actually mean during the Monte Carlo steps. I thought the temperature varies during those steps.
Can someone either explain this to me and point me to a easy to understand paper?
Thank you!
L.
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AbinitioRelax - Error with flags
Submitted by jmschu on Wed, 2018-11-21 17:36
Category:
Structure prediction
Hi folks,
I am attempting to run the AbinitioRelax application and when I use the -abinitio:relax option it returns an error.
Here are my commands: /home/xxxx/Documents/rosetta/main/source/bin/AbinitioRelax.default.linuxgccrelease @flags
where flags file contains:
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Is it better to have smaller nstruct but many runs?
Submitted by Loki01 on Mon, 2018-11-19 11:50
Category:
Loop Modeling
Hello,
wanted to ask whether it is better to have nstruct = 200 and create a 10 000 decoys using 50 different runs with different random seed or whether one can have 10 runs of nstruct = 1000. Does it matter?
Thank you!
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