Date: Mon, 2 Jan 2023 14:54:56 +0530
Dear Vinicius,
The following command worked for me.
But as you can see, the graph is crowded with the big label.
Is it possible to use fitpkaeo.py to modify the gnuplot file directly or
use the terminal output to generated the graph from scratch?
Please suggest. thank you and best regards.
Vaibhav
for file in $(ls 4LYT.pH*.cpin | sed 's/.cpin//g'); do cphstats -i
$file.cpin $file.cpout; done | fitpkaeo.py --graph
GL4 7: pKa = 3.86639 (+- 0.00579 ) ; Hill coefficient = 1.062 (+-
0.015 )
HIP 15: pKa = 6.51802 (+- 0.00140 ) ; Hill coefficient = 1.319 (+-
0.004 )
AS4 18: pKa = 1.91935 (+- 0.05141 ) ; Hill coefficient = 0.948 (+-
0.102 )
GL4 35: pKa = 6.25400 (+- 0.01561 ) ; Hill coefficient = 1.203 (+-
0.046 )
AS4 48: pKa = 1.27043 (+- 0.04681 ) ; Hill coefficient = 2.836 (+-
0.484 )
AS4 52: pKa = 2.43253 (+- 0.02384 ) ; Hill coefficient = 1.711 (+-
0.085 )
AS4 66: pKa = -0.39896 (+- 2.05629 ) ; Hill coefficient = 0.208 (+-
0.187 )
AS4 87: pKa = 2.66418 (+- 0.02418 ) ; Hill coefficient = 1.003 (+-
0.046 )
AS4 101: pKa = 3.83502 (+- 0.17970 ) ; Hill coefficient = 0.802 (+-
0.238 )
AS4 119: pKa = 2.77572 (+- 0.06012 ) ; Hill coefficient = 0.845 (+-
0.088 )
Graph generated to ./graph.png
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 Mon, Jan 2, 2023 at 12:22 PM Vinicius Wilian Cruzeiro <
vwcruz.stanford.edu> wrote:
> Hello Vaibhav,
>
> In your for loop you need to provide the cpout files from the simulation,
> not the *calcpka.dat files.
>
> Best,
>
> *Vinícius Wilian D. Cruzeiro, PhD*
> Postdoctoral Researcher
> Department of Chemistry
> Stanford University
> Twitter: .vwcruzeiro
>
> On Jan 1, 2023, at 8:31 PM, Vaibhav Dixit <vaibhavadixit.gmail.com> wrote:
>
>
> 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!
>>
>> *Vinícius 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
>> _______________________________________________
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>>
>
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(image/png attachment: graph.png)
