[gmx-users] How to calculate the number of ligand and water molecules around protein?

Pandya, Akash akash.pandya.15 at ucl.ac.uk
Fri Jan 24 21:12:26 CET 2020


Hi all,

I wanted to ask about the best way to calculate the number of ligand molecules and water molecules around my protein at certain cut-off. I have used gmx trjorder -nshell  and               gmx select -os. Both have given me different results, so I wanted to know if anyone has had any luck with either to an accurate degree? Any guidance will be much appreciated.

Akash


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