On Tue, Mar 09, 2021, Ming Tang wrote:
>
>May I ask is there a command in Amber that can insert a number of molecules
>in a solvated protein box just like the insert-molecules command in
>Gromacs and packmol? I tried to treat my molecules as ions and use addions
>command. The molecules were added successfully and they are all placed
>outside of the solvated box and very far away from the protein.
AmberTools includes a copy of packmol, and I think people are increasingly
using that to create initial simulations. Amber's AddtoBox command is
another alternative to addIons.
...good luck...dac
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Received on Tue Mar 09 2021 - 18:00:02 PST
