Yes sir. One trial run is available for both the aq and com systems. But,
how to obtain edgembar-amber2dats.py file ?
For loading FEToolkit I am following the steps as:
module load codes/amber22_gpu
source /apps/scratch/compile/amber22-gpu/amber22_src/FE-Workflow/
FE-Workflow.bashrc
source
/apps/scratch/compile/amber22-gpu/amber22_src/fe-toolkit/fetoolkit.module
But after that, when I type "setup_fe" command in /rbfe, then in
rbfe/results folder, DiscoverEdges.py, Expt.dat files got generated
automatically.
I am sharing DiscoverEdges.py file here ( which automatically generated).
Kindly give me suggestion.
Thanks & Regards
Kankana Bhattacharjee
On Fri, Aug 16, 2024 at 7:55 PM Shi Zhang <sz550.chem.rutgers.edu> wrote:
> Hello Kankana,
>
> Question #2 needs to be solved first, then the free energy results could
> be analyzed with FE-Toolkit.
>
> Based on your question #2, I assume you have already completed at least
> one trial for both "com" and "aq" phases. Following Tim's answers, try to
> use "edgembar-amber2dats.py" to extract energy information from those
> *ti.mdout. There is no need to rename any files. You will find a series of
> files with name dvdl*.dat and efep*.dat, and then you can proceed to
> analyze your simulations.
>
> Feel free to let us know if you have any further questions using the
> FE-ToolKit or FE-Workflow.
>
> Regards,
> Shi
>
> ------------------------------
> *From:* Timothy Giese <giese025.rutgers.edu>
> *Sent:* Friday, August 16, 2024 10:03 AM
> *To:* Kankana Bhattacharjee <kankana.bhattacharjee_phd21.ashoka.edu.in>;
> AMBER Mailing List <amber.ambermd.org>
> *Cc:* Shi Zhang <sz550.chem.rutgers.edu>; Ryan Snyder <
> rs2385.iqb.rutgers.edu>
> *Subject:* Re: [AMBER] FETookit analysis issue:
>
> My impression is that you are using the FE_Workflow scripts, which happen
> to use the FE-ToolKit programs to do some of the analysis. Based on the
> output, it looks like there's something wrong with the Workflow input. The
> DiscoverEdges.py script is expecting to find a subdirectory named
> "complex", but your directory is instead named "com". You could change line
> 26 of DiscoverEdsge.py so target="complex" instead reads target="com". You
> may need to also change reference="solvated" to reference="aq"; however,
> I'm not sure if DiscoverEdges.py was something that you wrote or if it was
> generated from the FE_Workflow scripts. If it was generated by the
> workflow, then there's something wrong there. The rest of the errors result
> from not having found the correct directory structure. For your second
> question, I'll have to refer you to either Shi or Ryan, whom I've CC'd.
> Personally, I've never used the workflow before so I'm not sure.
>
>
>
> ------------------------------
> *From:* Kankana Bhattacharjee via AMBER <amber.ambermd.org>
> *Sent:* Friday, August 16, 2024 3:10 AM
> *To:* AMBER Mailing List <amber.ambermd.org>
> *Subject:* [AMBER] FETookit analysis issue:
>
> Dear AMBER users,
>
> I am using AMBER22 version and completed the Advanced TI tutorial to mutate
> a ligand bound to a protein.
> 1. I am trying to analyse it using FEToolkit and for that I have loaded the
> required modules, but getting the error as:
> *setup_fe*
>
>
> User defined lambda schedule...
>
> The following lambda schedule will be used
> 0.00000000 0.10000000 0.20000000 0.30000000 0.40000000 0.50000000
> 0.60000000 0.70000000 0.80000000 0.90000000 1.00000000
>
>
>
> Lead ligand provided "" is not present in the list of transformations
> specified by the variable "translist"
> Ligand free energies will be expressed with respect to ligand with lowest
> free energy
>
>
>
> Running in analysis mode...
>
>
> Folder results/data/1h1q~1h1r/com already present. Skipping initial
> extraction.
>
> Folder results/data/1h1q~1h1r/aq already present. Skipping initial
> extraction.
> Running: python3 DiscoverEdges.py
> Traceback (most recent call last):
> File "./DiscoverEdges.py", line 26, in <module>
> edges = edgembar.DiscoverEdges(s,exclude_trials=exclusions,
> File
>
> "/apps/scratch/compile/amber22-gpu/amber22_src/fe-toolkit/build/local/lib/python3.8/site-packages/edgembar/DiscoverEdges.py",
> line 96, in DiscoverEdges
> raise Exception(f"target name manually set to '{target}',"
> Exception: target name manually set to 'complex', but no directories had
> that name
> Finished DiscoverEdges.py
>
> Running: edgembar-WriteGraphHtml.py -o analysis/Graph.html $(ls
> analysis/*~*.py)
> ls: cannot access analysis/*~*.py: No such file or directory
> usage: edgembar-WriteGraphHtml.py [-h] -o OUT [-s
> [{linear,mixed,nonlinear}]] [--exclude EXCLUDE [EXCLUDE ...]] [--refnode
> REFNODE] [-x EXPT]
> [-c CONSTRAIN [CONSTRAIN ...]]
> [--skip-outliers] [--shift-xgt-tol SHIFT_XGT_TOL] [--shift-xlt-tol
> SHIFT_XLT_TOL]
> [--avgcc-xgt-tol AVGCC_XGT_TOL]
> [--avgcc-xlt-tol AVGCC_XLT_TOL] [--maxcc-xgt-tol MAXCC_XGT_TOL]
> [--maxcc-xlt-tol MAXCC_XLT_TOL]
> [--lmi-xgt-tol LMI_XGT_TOL] [--lmi-xlt-tol LMI_XLT_TOL] [--dufe-xgt-tol
> DUFE_XGT_TOL]
> [--dufe-xlt-tol DUFE_XLT_TOL]
> [--errmsgs-xgt-tol ERRMSGS_XGT_TOL] [--errmsgs-xlt-tol ERRMSGS_XLT_TOL]
> edge.py [edge.py ...]
> edgembar-WriteGraphHtml.py: error: the following arguments are required:
> edge.py
> Finished creating analysis/Graph.html
>
> Running: edgembar-WriteGraphHtml.py -o analysis/GraphWithExpt.html -x
> ExptVals.txt $(ls analysis/*~*.py)
> ls: cannot access analysis/*~*.py: No such file or directory
> usage: edgembar-WriteGraphHtml.py [-h] -o OUT [-s
> [{linear,mixed,nonlinear}]] [--exclude EXCLUDE [EXCLUDE ...]] [--refnode
> REFNODE] [-x EXPT]
> [-c CONSTRAIN [CONSTRAIN ...]]
> [--skip-outliers] [--shift-xgt-tol SHIFT_XGT_TOL] [--shift-xlt-tol
> SHIFT_XLT_TOL]
> [--avgcc-xgt-tol AVGCC_XGT_TOL]
> [--avgcc-xlt-tol AVGCC_XLT_TOL] [--maxcc-xgt-tol MAXCC_XGT_TOL]
> [--maxcc-xlt-tol MAXCC_XLT_TOL]
> [--lmi-xgt-tol LMI_XGT_TOL] [--lmi-xlt-tol LMI_XLT_TOL] [--dufe-xgt-tol
> DUFE_XGT_TOL]
> [--dufe-xlt-tol DUFE_XLT_TOL]
> [--errmsgs-xgt-tol ERRMSGS_XGT_TOL] [--errmsgs-xlt-tol ERRMSGS_XLT_TOL]
> edge.py [edge.py ...]
> edgembar-WriteGraphHtml.py: error: the following arguments are required:
> edge.py
> Finished creating analysis/GraphWithExpt.html
>
> Kindly help me with this.
> 2. Also, it is said to transfer the "ti.mdout" files of both the aq and com
> states, so I would like to know should I have to rename separately the
> ti.mdout files for com and aq states or else how will it would be
> recognized as com and aq states (i.e from the *ti.mdout files) ?
>
> Your suggestions would be highly appreciated.
>
> Thanks & Regards
> Kankana Bhattacharjee
> Ph.D. Scholar
> Department of Chemistry
> Ashoka University
> Sonipat, Haryana
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Received on Fri Aug 16 2024 - 08:30:02 PDT
