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Scoring

Inconsistencies in full atom energy calculations

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Scoring

Hello,

I'd like to decompose the energy in one body energy terms (for each residue) and pairwise energy terms for residue-residue interactions.
I tried to check if I could decompose these terms and sum them up to retrieve the score returned by the scoring function.
The problem is that I try 3 different ways of computing the energy, and I get 3 different numbers.
Could someone please tell me what's wrong ?

Here is my code:

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Approximating CHARMM energy by the rosetta scoring function

Category: 
Scoring
PyRosetta

Is it possible to approxmate the CHARMM energy (function) by the rosetta scoring function?

As a starting point I could work with fixed angles and bond lengths, so I guess setting the weghts for fa_atr, fa_rep and fa_elec to 1 and all the rest to zero is a good start. But is it possible to somehow load the CHARMM diheral parameters?

Thank you for your help,
Ajasja Ljubetič

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MPI nodes hanging and output log incomplete

Category: 
Scoring

I'm using MPI with the PeptideDeriver pilot app (which I reworked to support JD2). I am running into some problems:

1. nodes that have finished jobs stall with 100% cpu usage while the entire MPI run isn't complete.
2. some tracer.log files don't contain all of the output -- for instance, the master node might have gotten a success message from a node, but not all the output of that job appear in the tracer.log file (the last bit is missing)
3. some jobs aren't finishing.

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can't find standard or standard.wts in weights folder (?)

Category: 
Scoring

Mac OS 10.7, 64 bit (i7 processor)
Python version 2.75 (version 3.4.1 also installed)

Hey, new to both PyRosetta, Python, and molecular modeling in general, but I found the PyRosetta User's Guide and have been working through it-until I ran into an issue with the scoring functions.

It seems that the software cannot find the standard or the standard.wts file in the weights folder which is supposed to be used for creating scoring functions. Specifically, when I try the following sequence of commands:

-In [23]: name='standard'

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using Rosetta to compute pH dependent binding?

Category: 
Scoring

We are interested in creating a protein that will bind to a hormone at physiological pH, but unbind to the hormone at acidic pH, encountered when the complex is cycled through the cell. To do this, we would like to use the pH_mode functionality developed by Kilambi and Gray (Biophys Journal 103:587-595, 2012).

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ddg_monomer and membrane proteins

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Scoring
Membrane

Dear all,
I am a new Rosetta (3.5) user and I would like to study the effects of some point mutations on a monomeric transmembrane protein.

Can ddg_monomer properly predict the change in stability induced by point mutations in transmembrane proteins? If yes, should I specify a particular score function file using -ddg:minimization_scorefunction option? I would like to study mutations in both, the transmembrane (membrane-facing and not) and the extracellular region of the protein, should I treat them separately?

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