> it won't hurt to learn about netCDF in python for sure.
It might hurt, but it could be a good pain in a way. Still, better to
know the longer paths for future reference than to take them. :-)
On 8/18/20 4:31 AM, 李奕言 wrote:
> Thanks for the advise.
> The problem has been solved by simply stripping the unwanted atoms in the topology file using ParmEd module in Amber, though it won't hurt to learn about netCDF in python for sure.
>
>> -----Original Messages-----
>> From: "Bill Ross" <ross.cgl.ucsf.edu>
>> Sent Time: 2020-08-16 16:56:15 (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
>>
>> 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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>> --
>> Phobrain.com
>>
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Received on Tue Aug 18 2020 - 05:00:03 PDT
