The "edgembar-amber2dats.py" is one command which can be issued directly in the commandline after loading the fetoolkit module, just like "setup_fe". It seems the DiscoverEdges.py file is blocked here, you can send it to me off the Amber mailing list.
Shi
________________________________
From: Kankana Bhattacharjee <kankana.bhattacharjee_phd21.ashoka.edu.in>
Sent: Friday, August 16, 2024 11:17 AM
To: Shi Zhang <sz550.chem.rutgers.edu>
Cc: AMBER Mailing List <amber.ambermd.org>; Ryan Snyder <rs2385.iqb.rutgers.edu>; Timothy Giese <giese025.rutgers.edu>
Subject: Re: [AMBER] FETookit analysis issue:
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<mailto: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<mailto:giese025.rutgers.edu>>
Sent: Friday, August 16, 2024 10:03 AM
To: Kankana Bhattacharjee <kankana.bhattacharjee_phd21.ashoka.edu.in<mailto:kankana.bhattacharjee_phd21.ashoka.edu.in>>; AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
Cc: Shi Zhang <sz550.chem.rutgers.edu<mailto:sz550.chem.rutgers.edu>>; Ryan Snyder <rs2385.iqb.rutgers.edu<mailto: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<mailto:amber.ambermd.org>>
Sent: Friday, August 16, 2024 3:10 AM
To: AMBER Mailing List <amber.ambermd.org<mailto: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 - 09:00:02 PDT
