Dear Pitambar
I corrected the input file(added a comma), but the problem persists.
Please, someone who has faced this, kindly reply.
Thank you
Priyasha
On 2025-06-28 00:08, Pitambar Poudel wrote:
> Not sure! But you seem to be missing a comma after the ntr flag.
>
> Pitambar Poudel
> Graduate Research Assistant
> Computational Biophysics and Bioinformatics Lab
> Department of Physics and Astronomy, Clemson University
> _Lab: http:/compbio.clemson.edu/ [1]_
>
> On Fri, Jun 27, 2025 at 8:36 AM Priyasha Majee via AMBER
> <amber.ambermd.org> wrote:
>
>> The job is still not working. I will attach the output and log file.
>>
>> Thank you
>>
>> Priyasha
>>
>> On 2025-06-27 17:30, Carlos Simmerling wrote:
>>
>>> As the message at the end of the output states, there is an error in
>>> reading the namelist. If you check each variable name carefully you
>>> will find that restraintmask is the proper name. These are listed in
>>> the manual.
>>>
>>> On Fri, Jun 27, 2025, 7:43 AM Priyasha Majee <22d0186.iitb.ac.in>
>>> wrote:
>>>
>>> Here are my input files and output file for reference. kindly help me
>>> out with this.
>>>
>>> Thank You
>>>
>>> Regards,
>>>
>>> Priyasha
>>>
>>> On 2025-06-27 16:56, Carlos Simmerling wrote:
>>>
>>> Reply to the amber list, not me.
>>> Make sure you look at the output files. Otherwise nobody will have
>>> any
>>> idea.
>>>
>>> On Fri, Jun 27, 2025, 7:08 AM Priyasha Majee <22d0186.iitb.ac.in>
>>> wrote:
>>>
>>> Thank you for the response.
>>>
>>> Tried without MPI. its still showing the same error. Should I send
>>> you
>>> my heating input?
>>>
>>> Thank you in advance.
>>>
>>> Priyasha
>>>
>>> On 2025-06-27 15:43, Carlos Simmerling wrote:
>>>
>>> Try without mpi. Also look in the mdout file.
>>>
>>> On Fri, Jun 27, 2025, 5:30 AM Priyasha Majee via AMBER
>>> <amber.ambermd.org> wrote:
>>>
>>> Dear All,
>>>
>>> I am trying to run MD equilibration on sander.MPI but every time it's
>>> throwing the following error
>>> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
>>> with errorcode 1.
>>>
>>> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
>>> You may or may not see output from other processes, depending on
>>> exactly when Open MPI kills them.
>>>
>>> I checked my input file, command, and directories.
>>> Can someone help with this problem?
>>> Thanks in advance
>>> Priyasha
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Links:
------
[1]
http://compbio.clemson.edu/lab/
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Received on Fri Jun 27 2025 - 22:30:02 PDT
