Re: [AMBER] Number of atoms in the coordinate file does not match the parm file

From: Carlos Simmerling via AMBER <>
Date: Mon, 18 Jul 2022 10:34:26 -0400

> strip :Na+,Cl-,WAT,H

this command tells it to strip all residues with names that match (the ":"
is for residues).
this will not work for hydrogen atoms, since they are in many residues. You
also cannot use .H, since that would look for atoms named H (they have many
try this mask and see if it gives the correct atoms:
 strip (:Na+,Cl-,WAT | .H=)

the "ambmask" program is very useful to test a mask and see what it matches
in your system - see the manual for details. This will often make it very
clear why things aren't working.

On Mon, Jul 18, 2022 at 10:21 AM Saranya vasudevan via AMBER <> wrote:

> Hi users,
> I have been running a 20ns MD simulation of a protein-ligand complex,
> using ntwprt = 3550 to record only the protein atoms into the crd files.
> While analyzing the trajectories in cpptraj, I got the following
> message:
> Error: Number of atoms in NetCDF file (3550) does not match number
> Error: in associated topology (7128)!
> I tried to delete the hydrogen atoms in the topology file to regenerate
> a protein without hydrogen parm file by using following command
> parm topology.parm7
> strip :Na+,Cl-,WAT,H
> parmwrite out nowater_H.parm7
> still i cant able to remove the hydrogen atoms,Is there a way to
> troubleshoot this?
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Received on Thu Aug 04 2022 - 13:34:40 PDT
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