VMD-L Mailing List

From: MARIA MILANESI (maria.milanesi_at_cnr.it)
Date: Mon Jul 15 2024 - 04:06:27 CDT

Dear VMD community,
I’m trying to optimize the parametrization of a novel small molecule (52 atoms) using FFTK and ORCA. I have two questions:
A: During the water interaction step, I obtained a lot of water molecules, with some stacked with other water molecules and some with the small molecule. Is that normal? How should I proceed?
B: In the meantime, I have run the quantum chemistry calculations of the obtained input files from the water interaction steps. I encountered two errors:
1. For only one input file (out of more than 70 files), I received the following error (all the others terminated normally):

ORCA finished by error termination in GSTEP
Calling Command: /work/y07/shared/apps/core/orca/5.0.3/orca_gstep MD4-DON-C18.ginp.tmp
[file orca_tools/qcmsg.cpp, line 465]:
.. aborting the run

2. I have tried to run the charge optimisation step, (I didn’t inserts the files MD4-DON-C18.ginp.tmp MD4-ACC-C18.ginp.tmp). And I obtain this error:

atomselect set: 0 data items doesn't match 1 selected atoms.
atomselect set: 0 data items doesn't match 1 selected atoms.
    while executing
"$temp set x [lindex [lindex $molCoords $i] 0]"
    (procedure "::ForceFieldToolKit::ChargeOpt::optimize" line 191)
    invoked from within
"::ForceFieldToolKit::ChargeOpt::optimize"
    (procedure "::ForceFieldToolKit::gui::coptRunOpt" line 55)
    invoked from within
"::ForceFieldToolKit::gui::coptRunOpt "
    invoked from within
".fftk_gui.hlf.nb.chargeopt.runOpt invoke "
    invoked from within
".fftk_gui.hlf.nb.chargeopt.runOpt instate !disabled { .fftk_gui.hlf.nb.chargeopt.runOpt invoke } "
    invoked from within
".fftk_gui.hlf.nb.chargeopt.runOpt instate pressed { .fftk_gui.hlf.nb.chargeopt.runOpt state !pressed; .fftk_gui.hlf.nb.chargeopt.runOpt instate !disab..."
    (command bound to event)

If needed I can send all the input and output files.
Thanks in advance,
kind regards
Maria