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Loop Modeling

antibody modeling error

Category: 
Loop Modeling

Hi all:

      I am going to use antibody.default.linuxgccrelease to make a model for an antibody sequence.  The command I entered is ”antibody.default.linuxgccrelease -fasta mxp335.fasta -antibody::grafting_database  /home/mxp/apps/rosetta/tools/antibody >error1.log“.  I encountered the following error:

.......

core.conformation.Conformation: current variant for 207 CYD
core.conformation.util: [ ERROR ] Residue 10 was disulfide bonded but had no partner
caught exception 

Post Situation: 

Error with talaris2014.wts, which leads to a garbade scorefunction in loop modelling for protein-protein docking

Category: 
Loop Modeling

Dear Sir or Madam,

I got a one complicated problem, which took place during loop modelling for protein-protein docking. I carry out tasks from the Meiler tutorial for Rosetta.

Post Situation: 

input file for loop modeling

Category: 
Loop Modeling

Hello

I want to repair my missing residues by loop modeling. As it has shown In the demos and tutorial, I should have a file like x_missing_loop.pdb

it is like main pdb file of target protein BUT it hase something called table energy pose bellow it. How I should make this table energy pose. ???? tutorial has not said anything about making this table energy pose

I have attached that input file from demos, please explain how I can make table pose energy which is under cordinations data?

Post Situation: 

perturb_temp flag

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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Is it better to have smaller nstruct but many runs?

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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Relevant number of cycles of loop closure required

Category: 
Structure prediction
Design
Loop Modeling

Dear All,

I have been working on the Domain insertion module of Rosetta. I need to know what are the relevant number of cycles of loop closure I require to enter for larger domain sets. The domain Im inserting is around 175 aa long. I am having trouble launching the same using MPI in parallel, hence the single processor is taking days for the output. Wondered if anyone who has worked on it could suggest a feasible number for AnchoredPDBcretator and also for AnchoredDesign.

Vasavi.

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broker domain insertion

Category: 
Loop Modeling

Hi 

   I am trying to model c terminus of my protein while keeping the majority of N terminus structure fixed. I an using broker domain insertion for this purpose. in the domain_insertion.xml file, I need to provide topology file for my protein. How can I make the topology file?

 

Thank you

Dhiraj

Post Situation: 

log files

Category: 
Loop Modeling

Hello,

Could you tell me please how can I save a log file (or direct output in a log file) in rosetta? Normally, I would do "utility -options > log.file".

But when I run /bin/remodel.linuxgccrelease @flag_missing_loops > log.file, I get something different from when I run /bin/remodel.linuxgccrelease @flag_missing_loops.

Perhaps, there is a simple way to controll log files but I cannot find it for now.

Post Situation: 

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