<< Conformational sampling with NAMD >>

From: I. Camps (icamps_at_gmail.com)
Date: Sat Sep 05 2020 - 12:54:13 CDT

Dear all,

I am starting to work with NAMD.

One of the analysis I need to do is to compute the binding free energy of a
ligand interacting with a protein. To do such a task, I configured the CaFE
plugin in VMD (Github <https://github.com/HuiLiuCode/CaFE_Plugin> and
reference <https://doi.org/10.1093/bioinformatics/btw215>). It uses two
methods: (1) the mmpbsa procedure and (2) the LIE (linear interaction
energy) procedure.

For the LIE method, the program needs, as input, a file resulting from
running a conformational sampling study for the ligand.

My doubt: What is a conformation sampling and how it is
implemented/configured in NAMD?

I know packages that search the conformational space for a molecule and
generate a library of conformers using systematic and Monte Carlo searches
but have no clue about how molecular dynamics do that sampling.



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