The problem hasn't been solved
I am interested in docking a camelid VHH to antigen. As far as I can tell SnugDock requires both the heavy and light chains. (I know there will be some problems with my H3 loop.)
Does anyone know a work-around for this?
Hi,
I am working on an enzyme design project for which I want one of the glutamic acid of the catalytic site to be protonated at OE2 position. I manually did that using schrodinger but when I prepared the structure using relax protocol, the glutamic acid becomes deprotonated. How, I can get a specific glutamic acid (For eg position 43) to be protonated specifically at OE2?
Thanks in advance for help
BH
I came across an error below
[ERROR] EXCN_utility_exit has been thrown from: src/core/scoring/disulfides/FullatomDisulfideEnergyContainer.cc line: 624
Anyone have any idea on it?
I'll explain what I do, in case someone has a solution to my problem.
I am trying to perform a docking protein-protein, where, a membrane protein arranged in a lipid membrane and balanced with water and ions, should be bound to a protein.
I need to know how much these structures interfere with docking.
Any tips?
I've run Abinitiorelax but it fails in scoring process.
In the begining, It seems good i can see some matrix and other logs
But it gives error at last when scoring things working.
I dont know which part is wrong.
Here are exact error messages:
When submitting a sequence to the robetta Structure Prediction server I get several structures back, I would like to know these structures are the results of how many decoys? 25,000? 1,000,000? is the final result clustered? does robetta run ab initio the way we do on an HPC?
any details would help.
Hi,
I'm currently working on a loop modeling script in PyRosetta, for inclusion as a protocol in InteractiveRosetta. Essentially, the script takes a collection of protein fragments, attempts to insert them into a scaffold using AnchoredGraftMover, and scores each pose. The script works fine, but some time after it finishes running I'll get a message saying that libmini.so has stopped working. Does anyone have any idea why this could be happening? I've included the script below. I'm using PyRosetta 3.
Thanks,
Will
Why do I get a different packstat score after different runs of Interface analyzer on the same structure ?
How is packstat value actually calculated? What does it signify?
Hello,
I'm trying to load a .pdb file for an RNA molecule, change a single base in the molecule, and calculate the change in free energy. I was looking at this tutorial (http://graylab.jhu.edu/pyrosetta/downloads/documentation/PyRosetta_Tutorial_2012.pdf) and it doesn't work with newer versions of PyRosetta. Has anyone else done something like this? The documentation hasn't been very helpful so far for RNA (though it's relatively extensive for protein).