Hi David,
Thanks for your suggestions. The restraint energy is determine by the distance between the small molecules. May I ask how does amber determine the distance between two small molecules when there are 30 atoms in each IGR group? I wish to apply restraint on the IGR groups when any of the two atoms in the two IGR group are closer than 10 Å, is this doable?
Thanks,
Ming
-----Original Message-----
From: David A Case <david.case.rutgers.edu>
Sent: Wednesday, 10 March 2021 11:59 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] makeDIST_RST
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 Sun Mar 14 2021 - 01:30:02 PST
