On Sun, Feb 18, 2024, Kaleem Arshad wrote:
>
> Thanks a lot. It worked.
> One more thing, which residues should I restrain? Protein plus ligand or
> only protein?
Generally, an initial step of equilibration aims to optimize the solvent
molecules that were added by tleap (or some other code like Packmol or
AddToBox.) One would generally restrain everything whose positions you want
to keep relatively fixed during this process; that would usually include
ligands.
There is no one correct way to proceed. Here is a a discussion of a method
for getting stable simulations that has been examined in lots of different
systems:
%A D.R. Roe
%A B.R. Brooks
%T A protocol for preparing explicitly solvated systems for stable molecular dynamics simulations
%J J. Chem. Phys.
%V 153
%P 054123
%D 2020
....dac
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Received on Mon Feb 19 2024 - 08:00:02 PST
