Re: [AMBER] How do I use for namd .dcd file?

From: Jason Swails <>
Date: Sat, 12 Oct 2013 20:06:05 -0400

On Sat, Oct 12, 2013 at 1:31 PM, sudipta <> wrote:

> Hi Jason,
> another problem which I am facing during mmpbsa calculation. it is showing
> that the number of atoms in .prmtop file mismatches with the no of atoms in
> .inpcrd file which is generated by program.
> FATAL: NATOM mismatch in coord and topology files
> However, I am not clear about this. Please give some suggestions regarding
> this.

Find out if it is happening with your complex, receptor, or ligand topology
files and try to figure out why this mismatch is occurring.

Common mistakes include creating incompatible topology files to start with,
specifying an incorrect receptor_mask and/or ligand_mask (although using
the default masks helps in this case), and having some ions or water
molecules in your complex system that are stripped out by the default value
of strip_mask.

It helps to understand the workflow that does behind the scenes,
as it helps when trying to debug these types of problems.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Sat Oct 12 2013 - 17:30:02 PDT
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