Re: [AMBER] Need help in Targeted MD

From: Jason Swails <>
Date: Mon, 05 Jan 2015 08:22:56 -0500

On Mon, 2015-01-05 at 18:34 +0530, Pallavi Mohanty wrote:
> Yes i know that the total number of atoms are different in constraint
> coordinates and prmtop file. Although total number of residues in the two
> systems are same but the total number of atoms are different because of
> different conformations of the protein(open and closed) and hence different
> number of water molecules in the box. While running the simulations I
> specified target(closed conformation) under the -ref flag.
> my worry is how to fix the NATOM mismatch, do i need to edit the inpcrd
> file and stripoff excess water manually?

You can use cpptraj to do that, but yes, that is what you need to do.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Jan 05 2015 - 05:30:03 PST
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