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

From: Daniel Roe via AMBER <>
Date: Fri, 22 Jul 2022 10:25:46 -0400


On Mon, Jul 18, 2022 at 10:21 AM Saranya vasudevan via AMBER
<> wrote:
> using ntwprt = 3550 to record only the protein atoms into the crd files.
> 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

This isn't what you want. The ntwprt flag saves only the first ntwprt
atoms (it is *not* removing hydrogens). So you want to keep those
atoms and remove the rest. Also, the 'strip' command only affects
topologies for subsequent actions. If you want to permanently modify
the topology you should use 'parmstrip', e.g.:

parm topology.parm7
parmstrip !(.1-3550)
parmwrite out nowater.parm7


PS - The reason there is a separate 'parmstrip' command is because if
you permanently modify a topology it will no longer match up with
input trajectories.

> 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 - 13:35:26 PDT
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