Thank you very much for this information!
So I've just added -nc =1 and it works fine!
Could you tell me in what cases should I additionally add the option
for multiplicity for the Antechamber ?
Many thanks in advance
Cheers
Enrico
Il giorno gio 6 ott 2022 alle ore 17:33 Dr. Anselm Horn via AMBER
<amber.ambermd.org> ha scritto:
>
> 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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>
>
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Received on Thu Oct 06 2022 - 09:00:03 PDT
