[gmx-users] All water molecules inside protein

David van der Spoel spoel at xray.bmc.uu.se
Sun Feb 3 11:46:58 CET 2019

Den 2019-02-03 kl. 11:09, skrev Dawid das:
> Dear Gromacs Users,
> I need to extract gro or pdb file with single snapshot from a trajectory
> for a protein inside solvation box. In the output, I need whole protein
> structure + all water molecules "inside" the protein. That could also mean
> all water molecules within let's say 0.3 nm distance from any atom
> belonging the protein. What is a simple and effective way to find only
> those water molecules which are within 0.3 nm distance from protein, please?
> Best wishes,
> Dawid Grabarek
gmx trjorder

David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.

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