From: brian.radak_at_gmail.com
Date: Wed Sep 07 2022 - 08:25:46 CDT
Please send pynamd and NAMD cph related questions to the listserv.
The error message you are seeing seems rather straightforward -- the
path to the JSON config file is not valid. Did you take this path from
the tutorial? The relevant file should be distributed with NAMD in the
toppar directory, but its absolute location will depend on where you
installed NAMD.
HTH,
Brian
-------- Forwarded Message --------
Subject: Error while analyzing testcph.log file by using pynamd
Date: Tue, 6 Sep 2022 19:21:32 +0530
From: Ankita Dhiman <dhimaniph_at_gmail.com>
To: brian.radak_at_gmail.com
Dear Sir,
We are trying to analyze results of NAMDCpH but getting the following
error after using command as written below:::
*Command:*
cphanalyze test.cphlog --json /toppar/conf_cph36_prot.json
Traceback (most recent call last):
File "cphanalyze", line 117, in <module>
tset = TitratableSystemSet.from_cphlogs(args.cphlog, args.json,
File "/usr/local/lib/python3.8/dist-packages/pynamd/cphlog.py", line
352, in from_cphlogs
tsys = TitratableSystem.from_cphlog(cphlog, configfiles)
File "/usr/local/lib/python3.8/dist-packages/pynamd/cphlog.py", line
1186, in from_cphlog
json_data = TitratableSystem.read_json(*configfiles)
File "/usr/local/lib/python3.8/dist-packages/pynamd/cphlog.py", line
1178, in read_json
json_data.update(json.load(open(configfile, 'r')))
FileNotFoundError: [Errno 2] No such file or directory:
'/toppar/conf_cph36_prot.json'
-- With Regards, Ankita Dhiman ICMR-Senior Research Fellow c/o Dr. Rituraj Purohit Principal Scientist Division Biotechnology CSIR-IHBT Palampur (H.P.)
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