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

From: Saranya vasudevan via AMBER <amber.ambermd.org>
Date: Mon, 18 Jul 2022 16:21:00 +0200

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

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 - 13:34:39 PDT
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