Enrico,
antechamber assumes a default charge of 0 for the ligand system.
If your ligand has a different total molecular charge, you have to tell
antechamber via the flags the tool mentions itself (see the output).
When applying quantum mechanics it makes a difference if you have a
closed-shell system (=even number of electrons) or not. This is, why
there is also a flag for multiplicity.
Most often, however, an odd number of electrons signals a problem with
the input, since most ligands are closed-shell systems.
And just from the atomic constitution, the total molecular charge is not
clear, several electronic configurations are possible - so the tool
wants you to specify explicitely, which you want.
>From what you described adjusting the total charge by adding -nc 1
should solve the problem.
Maybe that helps.
Best,
Anselm
Am 06.10.2022 um 16:38 schrieb Enrico Martinez via AMBER:
> Dear Amber Users!
> Using leaprc.gaff force field, I am trying to parametrize an organic
> ligand molecule that has +1 total charge due to the presence of an
> extra proton compared to it's uncharged version.
>
> Here is the error from antechamber:
> Running: /home/enrico/amber22/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
> ANTECHAMBER_AC.AC -p gaff
> Info: Total number of electrons: 151; net charge: 0
> Info: The number of electrons is odd (151).
> Please check the total charge (-nc flag) and spin multiplicity (-m flag).
>
> Running: /home/enrico/amber22/bin/sqm -O -i sqm.in -o sqm.out
> /home/enrico/amber22/bin/wrapped_progs/antechamber: Fatal Error!
> Cannot properly run "/home/enrico/amber22/bin/sqm -O -i sqm.in -o sqm.out".
>
> What is the total charge flag (-nc) and should it be manually modified
> for the parametrization of the charged ligand in order to resolve such
> an issue ?
> Many thanks in advance
> Cheers
> Enrico
>
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Received on Thu Oct 06 2022 - 09:00:03 PDT
