Dear Vinicius,
I tried your suggestion, but it is giving another error.
I tried one file at a time, but that also gives me just usage and doesn't
tell me what is wrong with my usage of cphstats command.
Please have a look and help me understand what changes I should make to the
command line options sot hat it recognizes the format of input and output
files.
thank you and best regards.
Vaibhav
(Happy new year to you and all members of the amber community)
(myseekr2) [vaibhav.hpc cnstpH-production]$ cphstats -i 4LYT.pH0.cpin -o
test.out
Usage: cphstats [-O] [-V] [-h] [-i <cpin or cpein>] [-t] [-o FILE] [-R FILE
-r INT]
[--chunk INT --chunk-out FILE] [--cumulative --cumulative-out
FILE]
[-v INT] [-n INT] [-p|-d] [--calcpka|--no-calcpka] [--fix-remd]
[--population FILE] [-c CONDITION -c CONDITION -c ...]
[--conditional-output FILE] [--chunk-conditional FILE]
cpout1 [cpout2 [cpout3 ...] ]
(myseekr2) [vaibhav.hpc cnstpH-production]$ for cpout_file in $(ls
*calcpka.dat); do cphstats -i *.cpin $cpout_file; done | fitpkaeo.py
Did not recognize the format of cpout 4LYT.pH0.cpin.
Error: Cpout file 4LYT.pH0.cpin is invalid! Skipping.
Did not recognize the format of cpout 4LYT.pH1.cpin.
Error: Cpout file 4LYT.pH1.cpin is invalid! Skipping.
Did not recognize the format of cpout 4LYT.pH2.cpin.
Error: Cpout file 4LYT.pH2.cpin is invalid! Skipping.
Did not recognize the format of cpout 4LYT.pH3.cpin.
Error: Cpout file 4LYT.pH3.cpin is invalid! Skipping.
Did not recognize the format of cpout 4LYT.pH4.cpin.
Error: Cpout file 4LYT.pH4.cpin is invalid! Skipping.
Did not recognize the format of cpout 4LYT.pH5.cpin.
Error: Cpout file 4LYT.pH5.cpin is invalid! Skipping.
Did not recognize the format of cpout 4LYT.pH6.cpin.
Error: Cpout file 4LYT.pH6.cpin is invalid! Skipping.
Did not recognize the format of cpout 4LYT.pH7.cpin.
Error: Cpout file 4LYT.pH7.cpin is invalid! Skipping.
Did not recognize the format of cpout pH0_calcpka.dat.
Error: Cpout file pH0_calcpka.dat is invalid! Skipping.
Error: Number of Cpout files 0 does not equal number specified: 9
Did not recognize the format of cpout 4LYT.pH0.cpin.
Regards,
Dr. Vaibhav A. Dixit,
Asst. Prof., Department of Medicinal Chemistry,
National Institute of Pharmaceutical Education and Research, Guwahati
(NIPER-G), Sila Katamur (Halugurisuk), P.O.: Changsari, Dist: Kamrup, Pin:
781101, Assam, India
Mob. No. +91-7709129400,
Email: vaibhav.niperguwahati.in; vaibhavadixit.gmail.com
https://niperguwahati.ac.in/DOC/profile/dixit.pdf
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
NCBI bibliography:
https://www.ncbi.nlm.nih.gov/myncbi/1Jgo56b26_AYKd/bibliography/public/
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
Please consider the environment before printing this e-mail
On Fri, Dec 30, 2022 at 9:36 PM Vinicius Wilian Cruzeiro <
vwcruz.stanford.edu> wrote:
> Hello Vaibhav,
>
> Is it referring to a file from the previous command?
> (cphstats -i 4LYT.equil.cpin ${ph}/4LYT.md1.cpout -o pH${ph}_*calcpka*.dat
> --population pH${ph}_populations.dat)
>
>
> Yes, it is referring to this command. The cphstats command will generate
> the pH${ph}_*calcpka*.dat files. Are you not getting these files?
>
> In your script, you are looking for a file called titration_curves.dat
> that apparently does not exist. The cphstats command is not creating any
> file with this name.
>
> A helpful tip: Amber has tools to help you plot titration curves. Search
> on the Amber manual for fitpkaeo.py. Or execute: fitpkaeo.py --help; and
> then: fitpkaeo.py --usage
>
> I hope this helps,
>
> Happy new year!
>
> *VinÃcius Wilian D. Cruzeiro, PhD*
> Postdoctoral Researcher
> Department of Chemistry
> Stanford University
> Twitter: .vwcruzeiro
> ------------------------------
> *From:* Vaibhav Dixit via AMBER <amber.ambermd.org>
> *Sent:* Thursday, December 29, 2022 8:07 PM
> *To:* AMBER Mailing List <amber.ambermd.org>
> *Cc:* Jason Swails <jason.swails.gmail.com>
> *Subject:* [AMBER] error with titration curve in Constant pH tutorial
>
> Dear Amber users and experts,
> I ran the constant pH tutorial
> <http://ambermd.org/tutorials/advanced/tutorial18/section4.php> which ran
> smoothly till the production and cphstats step.
> But I'm getting errors while trying to plot titration curves and gnuplot
> complaints about the missing titration_curves.dat file.
>
> The tutorial mentions about "computing pKa values using the output from
> calcpka. "
> I can't find calcpka in the path and it wasn't used in previous steps of
> the tutorial.
> Is it referring to a file from the previous command?
> (cphstats -i 4LYT.equil.cpin ${ph}/4LYT.md1.cpout -o pH${ph}_*calcpka*.dat
> --population pH${ph}_populations.dat)
>
> I'm assuming that the font error is not fatal here.
> Please help me understand how to fix this error so that I can proceed to
> prepare my system with non-standard titrable residues (Heme).
> Thanking you in advance and best regards.
> Vaibhav
>
> (base) [vaibhav.hpc cnstpH-production]$ gnuplot titration_curves.gpi
> fontconfig: Didn't find expected font family. Perhaps URW Type 1 fonts need
> installing? when opening font Helvetica, trying default
> "titration_curves.gpi" line 23: warning: Cannot find or open file
> "titration_curves.dat"
>
> fit f(x) 'titration_curves.dat' using 1:2 via n,pka
> ^
> "titration_curves.gpi" line 23: Can't read data from
>
> (base) [vaibhav.hpc cnstpH-production]$ ls -arlht
>
> Regards,
>
> Dr. Vaibhav A. Dixit,
>
> Asst. Prof., Department of Medicinal Chemistry,
>
> National Institute of Pharmaceutical Education and Research, Guwahati
> (NIPER-G), Sila Katamur (Halugurisuk), P.O.: Changsari, Dist: Kamrup, Pin:
> 781101, Assam, India
>
> Mob. No. +91-7709129400,
> Email: vaibhav.niperguwahati.in; vaibhavadixit.gmail.com
> https://niperguwahati.ac.in/DOC/profile/dixit.pdf
> https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
>
> ORCID ID: https://orcid.org/0000-0003-4015-2941
>
> NCBI bibliography:
> https://www.ncbi.nlm.nih.gov/myncbi/1Jgo56b26_AYKd/bibliography/public/
>
> http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
>
> Please consider the environment before printing this e-mail
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sun Jan 01 2023 - 21:00:02 PST
