[AMBER] Number of atoms in the coordinate file does not match the parm file when assigning ntwprt value

From: 李奕言 <liyiyan.pku.edu.cn>
Date: Sun, 16 Aug 2020 12:00:28 +0800 (GMT+08:00)

Dear all,

I have been running a 500 ns aMD simulation of a protein-membrane system, using ntwprt = 8873 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 NPTproductionAMD.crd (8873) does not match number in associated parmtop (95096)!

I tried to delete the non-protein atoms in the original pdb file and to regenerate a protein-only parm file, yet unfortunately I miscounted the number of atoms in the protein (8872) and an 8873 number of atoms resulted in a system of the entire protein plus a single carbon atom of the POPC lipid, which was automatically converted to a full POPC molecule by Leap. It seemed that the parm file with the corresponding 8873 atoms was not available for me.

Is there any way to fix it?

Thanks in advance!

Best regards,


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Received on Sat Aug 15 2020 - 21:30:02 PDT
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