Thank you very much!
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 Thu, Jan 5, 2023 at 2:24 AM Vinicius Wilian Cruzeiro <vwcruz.stanford.edu>
wrote:
> Hello Vaibhav,
>
> It is possible to modify the matplotlib commands inside the fitpkaeo.py
> script to make the plot the way you like. Another option you have is to get
> the raw data and plot it however you like:
>
> for file in $(ls 4LYT.pH*.cpin | sed 's/.cpin//g'); do cphstats -i
> $file.cpin $file.cpout; done
>
> I hope this helps.
>
> Best,
>
> *Vinícius Wilian D. Cruzeiro, PhD*
> Postdoctoral Researcher
> Department of Chemistry
> Stanford University
> Twitter: .vwcruzeiro
> ------------------------------
> *From:* Vaibhav Dixit <vaibhavadixit.gmail.com>
> *Sent:* Monday, January 2, 2023 1:24 AM
> *To:* Vinicius Wilian Cruzeiro <vwcruz.stanford.edu>
> *Cc:* AMBER Mailing List <amber.ambermd.org>
> *Subject:* Re: [AMBER] error with titration curve in Constant pH tutorial
>
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jan 05 2023 - 05:30:02 PST
