Re: [AMBER] error for mismatch NATOMS

From: Jason Swails <>
Date: Sat, 26 Sep 2020 14:50:12 -0400

The error message suggests that the number of atoms specified in the
coordinate/trajectory file for the complex is different than the number of
atoms in the resulting trajectory.

By default, the `strip_mask` variable in the input file will
strip out all of the metal atoms from the trajectory. You need to override
this value to *not* strip out the metal atom in your complex that you would
like to keep.


On Thu, Sep 24, 2020 at 2:28 AM Asmi Mahmood <> wrote:

> Hi I'm using AMBER for energy calculation of my system. In my
> protein- ligand system there is also a metal atom Nickle in the binding
> site. I used charmm-gui for PSF generation and ran simulations using
> NAMD. For MMPbsa, I used ambertools20. Converted all PSF and crd files into
> prmtop using commands in parmed of chamber: Chamber -top top.rtf -param
> file.prm - str file.str -psf file.psf -crd file .PDB
> Followed by outparm file.prmtop and inpcrd.
> All files generated successfully without any error. But when I ran MMPbsa
> command it gives error just after initializing GB calculation Calerr:
> complex.prmtop
> Detail of error in gb.out file is FATAL: mismatch NATOM in coordinate and
> topology file.
> For troubleshooting, I ran tutorial files it ran well. In addition I also
> ran an other NAMD simulated protein. It also ran without any error.
> I am confused how to sort it out.I checked number of atoms in complex PSF
> and PDB files atoms are same. I generted PSF files both by charmm-gui and
> also by vmd. Even then same error.My gut feel says it's something about the
> metal ion in the binding site.
> Plz guide me. Thanks in advance
> _______________________________________________
> AMBER mailing list

Jason M. Swails
AMBER mailing list
Received on Sat Sep 26 2020 - 12:00:03 PDT
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