Re: [AMBER] Need help in Targeted MD

From: Pallavi Mohanty <>
Date: Mon, 5 Jan 2015 18:34:02 +0530

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?

On Mon, Jan 5, 2015 at 6:04 PM, David A Case <>

> On Mon, Jan 05, 2015, Pallavi Mohanty wrote:
> > FATAL: NATOM mismatch in constraint coord and topology files.
> You set ntr=1, so the program will be reading constraint coordinates
> (specified with the -ref flag.) The number of atoms in this file does not
> match the number atoms in your prmtop file. You'll have to examine your
> input
> files to figure out why this is so.
> ....dac
> _______________________________________________
> AMBER mailing list

Pallavi Mohanty
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Received on Mon Jan 05 2015 - 05:30:02 PST
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