Dear Amber Users,
I encountered a fatal error while running a minimization using `pmemd.cuda`
in Amber22. The job aborts with the following message:
double free or corruption (out)
Program received signal SIGABRT: Process abort signal.
Backtrace for this error:
#0 0x15450b6a83ff in ???
#1 0x15450b6a837f in ???
#2 0x15450b692db4 in ???
#3 0x15450b6eb4e6 in ???
#4 0x15450b6f25eb in ???
#5 0x15450b6f438f in ???
#6 0x558a69 in ???
#7 0x5acd57 in ???
#8 0x5896bf in ???
#9 0x4bd2fc in ???
#10 0x15450b694492 in ???
#11 0x4d65cd in ???
#12 0xffffffffffffffff in ???
The command I used is:
pmemd.cuda -O -i minimization_solv.in -o minim_1/minim_1.out -p
trimer_solvated.prmtop -c trimer_solvated.inpcrd -r minim_1/minim_1.ncrst
-ref trimer_solvated.inpcrd -inf minim_1/minim_1.info
Some context:
- The system is a trimer solvated in a custom chloroform box built with
`tleap`.
- I used GAFF for the ligand and a pre-equilibrated chloroform box
(`CHCL3BOX`)
- The minimization input includes restraints (`ntr=1`) on the solute.
I’ve verified that:
- The `prmtop` and `inpcrd` files are correctly generated.
- The system contains 12480 atoms (from `ambpdb | grep -c '^ATOM'`).
I would appreciate any suggestions on what might cause this corruption or
steps I can take to debug or fix it.
Thanks
Devid
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Received on Tue May 06 2025 - 00:00:03 PDT
