> 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 - 01:30:03 PDT
