Re: [AMBER] prmtop file generated with CLOSEST in cpptraj

From: Daniel Roe <>
Date: Thu, 23 Dec 2021 09:22:38 -0500


On Wed, Dec 22, 2021 at 7:05 PM James Kress <> wrote:
> Why is this prmtop file generated when cpptraj CLOSEST command is used? Is

The 'closest' command will retain only the specified number of solvent
molecules (removing the rest), so the resulting topology will differ
from the original topology. The new topology corresponds to the new
pared-down system.

> it required for any future calculations on the system to which CLOSEST is

It's only necessary if you want to e.g. process an output trajectory
generated after the 'closest' command. If you use an output trajectory
format that has some topology information (like mol2) the topology
generated by 'closest' may be unnecessary (although it won't have
things like angle/nonbond/etc parameters).


> applied?
> Any insight would be appreciated.
> Thanks.
> Jim
> James Kress Ph.D., President
> The KressWorksR Institute
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Received on Thu Dec 23 2021 - 06:30:02 PST
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