Thank you for the reply.
Sorry for not making this clear.
It is the ntwprt value 8873 that did not correctly represent the protein molecule (8872 atoms).
The problem is how I can get a parm file with 8873 atoms (protein + one POPC carbon atom), or how I can change the NetCDF file into one that has 8872 atoms (sounds tricky).
Or else I just have to perform the simulation again with ntwprt = 8872 ?
Ian
> -----Original Messages-----
> From: "Bill Ross" <ross.cgl.ucsf.edu>
> Sent Time: 2020-08-16 12:21:03 (Sunday)
> To: amber.ambermd.org
> Cc:
> Subject: Re: [AMBER] Number of atoms in the coordinate file does not match the parm file when assigning ntwprt value
>
> What if you retry deleting in a copy of the pdb. and this time count
> correctly?
>
> Bill
>
> On 8/15/20 9:00 PM, 李奕言 wrote:
> > 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
> --
> Phobrain.com
>
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Received on Sun Aug 16 2020 - 01:30:02 PDT
