Valdes-Tresanco-MS
commented
9 months ago We will keep it in mind for future versions. We will implement it in the analyzer. Regarding the selection of residues to print, we have multiple selection schemas. "within" works well for systems with small variations so that the initial structure of the trajectory is structurally close to the rest of the frames. Using "all" has the disadvantage of computational cost and the huge number of charts and interactions. We have manual selection by the user. If you are interested in selecting specific residues you can do so by defining them one by one, for example: print_res="A/1,3-10,15,100 B/25". In the documentation, we have other examples and more complete explanations (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/input_file/#decomp-namelist-variables) In general, it will save a little time, but probably imperceptible.
In which tool?
gmx_MMPBSA
New Feature
It would be nice to be able to suppress the ligand-ligand and receptor-receptor interactions displayed in the decomposition when done pairwise. I'm trying to generate a residue interaction network (single protein) where my edges are the interaction energies. My system has significant conformational change so using the "within" option leaves out useful interactions, but doing "all" does take forever to generate the data. Even for a 30 residue protein with ligand nearly 1000 interactions are displayed, and as you note in the documentation most of these interactions are inconsequential. Chunking the receptor is a workaround, but this option may be useful for others.
Of course, I don't know if it would actually save any time not having to generate the intraligand and intrareceptor interactions to print.
Description
No response
Relevance
low
Difficulty to implement
low