VMD-L Mailing List

From: Gumbart, JC (gumbart_at_physics.gatech.edu)
Date: Sun Jul 21 2024 - 22:13:21 CDT

Hi Maria,

A: The calculations should be run one water at a time, but I guess what you’re seeing is just all the individual calculations loaded at once. You don’t need to visualize them to proceed with the optimization, but it’s useful to see in case a water moves far away from the molecule, in which case you should minimize its weight in the optimization.

B1: I’m a little concerned that you have 70 input files for only 52 atoms? There should be one for each hydrogen bond donor or acceptor and occasionally two (iirc) for carbonyl oxygens. So if FFTK is really generating so many, you may want to look for why. I have never used ORCA though and can’t comment on why it fails.

B2: I think this means one or more of the ORCA output files is malformed somehow and the molecule is not being read in properly. The visualization will give you a clue.

As a fallback, our support for Psi4 in FFTK is complete. The paper is here: https://urldefense.com/v3/__https://pubs.aip.org/aip/jcp/article-abstract/160/24/242501/3299296/Broadening-access-to-small-molecule__;!!DZ3fjg!-xB3jGvLWJ32JlaTSC9e3lryMSPJAFcsAnqcmHVF2P3EXLpeUJMQO-gV08kTtFGqzcLpLD2ihd_6w6Wq5BxqwUlrRmg$
and until it’s in a released version, you can replace your FFTK files in the plugins directory with these: https://urldefense.com/v3/__https://simbac.gatech.edu/fftk-July-2024.zip__;!!DZ3fjg!-xB3jGvLWJ32JlaTSC9e3lryMSPJAFcsAnqcmHVF2P3EXLpeUJMQO-gV08kTtFGqzcLpLD2ihd_6w6Wq5BxqOgxxYXM$

Best,
JC

On Jul 15, 2024, at 5:06 AM, MARIA MILANESI <maria.milanesi_at_cnr.it> wrote:

You don't often get email from maria.milanesi_at_cnr.it<mailto:maria.milanesi_at_cnr.it>. Learn why this is important<https://urldefense.com/v3/__https://aka.ms/LearnAboutSenderIdentification__;!!DZ3fjg!-xB3jGvLWJ32JlaTSC9e3lryMSPJAFcsAnqcmHVF2P3EXLpeUJMQO-gV08kTtFGqzcLpLD2ihd_6w6Wq5Bxq6j2S1Ic$ >
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