Dear AMBER Users and Developers,
I am writing to seek assistance with a persistent segmentation fault I am
encountering while following the "Parameter Fitting with mdgx" tutorial,
specifically at Stage 2 (Fitting Parameters). (
https://ambermd.org/tutorials/advanced/tutorial32/Part2.php)
To ensure a clean test, I followed the tutorial's instructions exactly. I
started in a new directory, downloaded the pristine files from the
tutorial's links (DistilledResults.tar.gz, Glycerol_vac.top, MPD_vac.top),
and used the original fit.in file to run the two-system (Glycerol + MPD)
parameter fit.
Unfortunately, the process still fails with a segmentation fault
immediately after the "adjustable terms mapped" line is printed. Here is
the terminal output:
mdgx -i fit.in
GetParamNamelist >> Warning. Unrecognized restraint scaling method
GetParamNamelist >> E... Valid methods are 'estimate' and 'spy.'
GetParamNamelist >> See the manual for descriptions. The default
GetParamNamelist >> 'estimate' method remains in effect.
mdgx >> Unique adjustable parameters enumerated.
mdgx >> 2 conformations read.
mdgx >> Parameter keys read.
mdgx >> 19 adjustable terms mapped.
Segmentation fault (core dumped)
For the sake of thoroughness, I have also previously attempted several
debugging steps:
1.
I ran a single-system test using only Glycerol.
2.
This produced "Torsion type ... not found" errors.
3.
Using ParmEd, I diagnosed and corrected atom type mismatches in the
input file (e.g., hc vs. h1).
4.
Even after correcting the input file for the single-system test, it
still resulted in the same segmentation fault.
The fact that the error persists even with the tutorial's exact, unmodified
setup and pristine files suggests the issue may be more fundamental than a
simple input file error. I suspect it could be related to my specific build
or environment. (System Information: AmberTools 25)
Could you offer any further advice or is this a known problem?
Thank you for your time and any guidance you can provide.
Sincerely,
JJS
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Received on Wed Sep 24 2025 - 00:00:03 PDT
