Molfile to Params File Issue
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Hello People,
I am not sure if this is the correct forum to ask this question, but I thought many people here would have knowlege to answer me.
Hello,
I am interested in modeling the changes to a protein after substitution of the unnatural amino acids L-ANAP and Aladan pictured below.
It does not appear that the params for these are packaged with Rosetta. However, is there an unofficial library/repository of Rosetta params that may contain params for these amino acids?
I have been stuck on the problem of generating rotamer libraries for a while now as I try to repeat the process for non-canonical residues (starting with the test case of ornithine [C40]). The original documentation for this process is provided at the following address:
https://www.rosettacommons.org/demos/latest/public/make_rot_lib/README
Hey everyone,
I am trying to design a protein with a covalent bond between the C of Thr and the N of Gly with a Tyr in between them (imitating the chromophore from GFP for perspective). Because of this odd 5-membered ring formation, I used Thr/Gly with a generous distance constraint between them in my CST file when I ran RosettaMatch to find likely sites in my scaffold proteins. My sites place the two backbone atoms ~4-5A apart.
I am working on developing my CST file for the protein I'm designing and I have a few questions about some of the additional constraints I've seen in the example CSTs mentioned in the user's manual.
Hello!
I want to use a molecule with retinal in Rosetta. I've read the documentation on this page
https://www.rosettacommons.org/demos/latest/public/design_with_ncaa/README
But I also wanted to ask if I can somehow use the retinal parametrisation I already have for namd. There it is written in the CHARMM Parameter File.
Thank you in advance,
Dmitrii.
Hello everyone,
I am trying to perform a B3protein design tests using rosettascript (rosetta demo model). I have 3 designable positions and I am interested in the functionalities of the movers:"RandomMutation" and "GreedyOptMutationMover"
Using these movers, none of my design positions have been taken into account as a designable! In the log file, there are warnings
indicating that there is no design position.
Is it possible to combine a flags file with command line arguments?
For example, something like this:
minimize_with_cst.linuxgccrelease -in:file:l min_pdb_file_list @flags_file
where flags_file contains additional options. Moreover, what is the effect of changing the order of command line arguments and flags files? Which takes precedence? That is, what is the difference between the above command and:
minimize_with_cst.linuxgccrelease @flags_file -in:file:l min_pdb_file_list
Thanks.