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 - 00:30:02 PDT
