Re: [AMBER] Unclear cphstats warning

From: He, Amy via AMBER <amber.ambermd.org>
Date: Mon, 19 Aug 2024 03:28:41 +0000

Hi Matthew!

I might be wrong, but I think this warning message often appears when there’s a problem with the first line in the cpout files, “Solvent pH”, which is, when the data in your cpout files contain a pH that’s not reported in the first line of any of the provided cpout files.
If you’re very sure that the data in your cpout files are correct, you can re-distribute the data by your own codes without looking at Solvent pH at the beginning.

Best regards, 


--
Amy He
Forli Lab . TSRI
yihe.scripps.edu
From: Guberman-Pfeffer, Matthew via AMBER <amber.ambermd.org>
Date: Sunday, August 18, 2024 at 12:02 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] Unclear cphstats warning
Dear AMBER community,
I ran a 4-way pH-REMD in two chunks (indexed as 0 and 1). When processing the output form the second of these chunks with the following command:
cphstats --fix-remd reordered_1 001/phremd_1.cpout 002/phremd_1.cpout 003/phremd_1.cpout 004/phremd_1.cpout
I get:
WARNING: not all data records were assigned to a specific cpout file
        this can happen, for instance, if you did *not* provide all
        of the replica cpout files to cphstats to process. Check
        your results carefully!
But I did provide the cpout file for each of the four replicas. Something else is presumably wrong. How can I figure out what is causing the warning? I’ve run the same command in other directories for differ 4-way replicas and many more chunks and get no warning. Something seems to have happened in this particular case.
Best,
Matthew
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!2mHqf4s1EGxhUbnMdvgWrUroyEwc4TvQW3kbNM9f6WUqXbn_pu_fWG0u8EMC4Ie-S_WnjCDPa1jo-OSJWEh9XU2h9j0$<https://urldefense.com/v3/__http:/lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!2mHqf4s1EGxhUbnMdvgWrUroyEwc4TvQW3kbNM9f6WUqXbn_pu_fWG0u8EMC4Ie-S_WnjCDPa1jo-OSJWEh9XU2h9j0$>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Aug 18 2024 - 20:30:02 PDT
Custom Search