I'd try python's netcdf if you don't where to start:
https://unidata.github.io/netcdf4-python/netCDF4/index.html
https://pypi.org/project/netCDF4/
Bill
On 8/16/20 1:27 AM, Bill Ross wrote:
> > how I can change the NetCDF file into one that has 8872 atoms
>
> I think it shouldn't be too hard to write a program using the NetCDF
> library to read 8873 * 3 numbers and write 8872 * 3 numbers. I haven't
> used NetCDF myself, but there will be examples of reading and writing it
> in the code.
>
> Bill
>
>
> On 8/16/20 1:21 AM, 李奕言 wrote:
>> 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 - 02:00:02 PDT
