Dear developers and users,
I compiled ambertools23 with QUICK support and successfully run QM/MM calculation on my system. My system contains protein ATP molecule with two Mg ions and druglike ligand. ATP parameters were obtained from Richard Bryce site (amber.manchester.ac.uk) and ligand was parametrized by openff sage2.1. I did standard MD using amber22 without any issues. QM/MM seems to be fine if I include ligand and Mg ions in QM region, but after including ATP in QM region calculation crashes with error:
At line 184 of file /home2/jurajdobias/QUICK/amber22_src/AmberTools/src/quick/src/modules/quick_sad_guess_module.f90 (unit = 212)
Fortran runtime error: Cannot open file '/home2/jurajdobias/QUICK/amber22/AmberTools/src/quick/basis/DEF2-SVP.SAD/': Is a directory
From .out file it seems, that 3 oxygens on last phosphate were not correctly identified as oxygens:
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 5963 Mg 0.8115 5.9113 1.4435
QMMM: 2 5964 Mg 2.7773 4.4252 -0.8689
QMMM: 3 5965 ^.^. 2.0451 4.5731 5.3015
QMMM: 4 5966 P 1.1880 5.4871 4.5387
QMMM: 5 5967 ^.^. 1.5994 5.7518 3.1545
QMMM: 6 5968 ^.^. 0.7944 6.6874 5.2830
My explanation is that amber is searching for basis set in DEF2-SVP.SAD/ directory, but for these oxygens, it is missing element information, therefore it is trying to open directory.
I am attaching input and output files.
Any help solving the issue would be greatly appreciated.
Juraj
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Received on Wed Jan 31 2024 - 02:00:02 PST
