Unsolved

Hello Everyone,

Does anyone know if it is possible to use InterfaceAnalyzer only on a subset of atoms instead of the whole proteins?

Specifically, I've recently completed 4x 2 us simulations in GROMACS and would like to understand how different positions/polar/hydrogen bonding networks of an interface loop affect interaction energy between the two proteins.

If this cannot be done, I suppose an alternative approach would be to strip all non-relevant residues with awk and then run only the subsets through InterfaceAnalyzer

Hello,

I am having problems with Design simply stalling at a specific step in a number of jobs I am running. I can recreate the error, but every time it happens the job stops here:

core.pack.task: Packer task: initialize from command line() 

I've checked the tasks of the computer I am running this on and it shows that Design is still running, and when I kill that specific job the Design run continues unperturbed. 

I've attached the appropriate log file. Any help would be greatly appreciated.

Hi.

I'm with a doubt in relation to setting the alpha carbon to the CaRMSD. Analyzing the tutorial(Mailerlab) understand: that fixed points are used, and in the case of an ion channel (from a RosettaCM) Ca of the first residue of the alpha helix and Ca last residue alpha helix.
You are correct my deduction?

Hello,

I'm debating whether I should use a movemap or the -pivot_residues flag to specify the flexible region in a backrub protocol. Movemap allows you to specify BB and CHI flexibility separately, but if I use BBCHI should I expect different performance vs -pivot_residues?

I would use -pivot_residues since it is simpler and I see examples recommending it here on the forum. However I'm comparing backrub performance to relax performance, and relax uses movemap but does not have the pivot-residues flag.