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Poltype 2: Automated Parameterization and Free Energy Prediction for AMOEBA
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xtb not included in environment.yml but called in parameterization #42

Closed blakemertz closed 7 months ago

blakemertz commented 7 months ago

I made it to the initial multipole and polarization step of my fragments for a small molecule I am trying to parameterize, and came across this error in my poltype.log file:

Wed Apr  3 19:26:07 2024 Normal termination: logfile=4_5_Index_0-opt-2-3-107_preQMOPTprefit.alz path=/media/bak11/modulus/MDH/poltype/MDH-195/Temp/Fragments/4_5_Index_0/qm-torsion
Wed Apr  3 19:26:07 2024 All jobs have terminated ['4_5_Index_0-opt-2-3-107_preQMOPTprefit.alz']
Wed Apr  3 19:26:13 2024 Percent of jobs finished 0.0, jobs left = 13
Wed Apr  3 19:26:13 2024 Submitting: /media/bak11/binaries/miniconda3/envs/xtbenv/bin/xtb --gfn 2 --chrg 0 --uhf 0 4_5_Index_0-opt-2-3-275_preQMOPTprefit_xyzformat.xyz --opt --input xtb-opt-2-3-275_constr.txt > xtb-opt-2-3-275.log path = /media/bak11/modulus/MDH/poltype/MDH-195/Temp/Fragments/4_5_Index_0/qm-torsion
/bin/sh: 1: /media/bak11/binaries/miniconda3/envs/xtbenv/bin/xtb: not found
Wed Apr  3 20:26:13 2024 Error Job has not been updated in 1 hours last update time = 1.0000298017889824 hours logname=/media/bak11/modulus/MDH/poltype/MDH-195/Temp/Fragments/4_5_Index_0/qm-torsion/xtb-opt-2-3-275.log
Wed Apr  3 20:26:14 2024 ERROR termination: logfile=/media/bak11/modulus/MDH/poltype/MDH-195/Temp/Fragments/4_5_Index_0/qm-torsion/xtb-opt-2-3-275.log path=/media/bak11/modulus/MDH/poltype/MDH-195/Temp/Fragments/4_5_Index_0/qm-torsion
Wed Apr  3 20:26:14 2024 Percent of jobs finished 7.69, jobs left = 12
Wed Apr  3 20:26:14 2024 Submitting: /media/bak11/binaries/miniconda3/envs/xtbenv/bin/xtb --gfn 2 --chrg 0 --uhf 0 4_5_Index_0-opt-2-3-303_preQMOPTprefit_xyzformat.xyz --opt --input xtb-opt-2-3-303_constr.txt > xtb-opt-2-3-303.log path = /media/bak11/modulus/MDH/poltype/MDH-195/Temp/Fragments/4_5_Index_0/qm-torsion
/bin/sh: 1: /media/bak11/binaries/miniconda3/envs/xtbenv/bin/xtb: not found

Xtb is supposed to be a fallback if psi4 times out, but I noticed that it is not listed in the .yml files provided in the Environment folder. Is this an oversight since xtb and xtb-python are in the conda-forge channel, or has xtb been dropped from poltype2 and this is a legacy call in the torsion step?

And why is poltype2 calling for xtb in a separate environment?

blakemertz commented 7 months ago

Shite! Nevermind, I must have skipped over the XTB conda environment snippet in the installation instructions. SMH.....