2
votes
Accepted
How to specify input resfile for Rosetta?
The problem is my pack.xml specified a resfile.txt location which over-wrote my command-line option.
...
- 153
2
votes
Accepted
How many models should be generated by rosetta for denovo protein structure prediction?
Unfortunately you do in general increase your chance of success by going to the 50k range of models or higher. Projects like Rosetta@home exist because even large research groups can't access as much ...
- 931
2
votes
Accepted
How to calculate various properties of a protein structure per atom using PDB2PQR and Rosetta tools (or any other tools)?
Per Atom
You are correct. Rosetta scorefunction does not store any per atom data. The scoring operates at the per residue level. Whereas each atom has its coordinates and properties in full atom mode, ...
- 4,074
1
vote
How are different forcefields developed/evaluated?
The Rosetta ref2015 is well described in two papers, which I wish I had read much earlier, see this JChIM paper.
It's a statistical forcefield, where the terms are weighted to best match the empirical ...
- 4,074
1
vote
How are different forcefields developed/evaluated?
Some force-fields rely solely on theoretical physical principles, while others are tweaked specifically for the goal of accurately depicting certain structures like sheets and helices or movement/...
- 151
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