I see. So essentially since I can't eliminate H and a partial charge of
zero is needed ,and set, for FEW I am stuck between a rock and a hard
place. Thanks again for you help!
On Nov 9, 2016 1:39 AM, "Hannes Loeffler" <Hannes.Loeffler.stfc.ac.uk>
wrote:
> Antechamber expects a complete structure so you will have to add all the
> hydrogens beforehand. The partial charges from the mol2 won't matter
> to antechamber.
>
> On Wed, 9 Nov 2016 01:26:49 -0700
> Miguel Rivera <miguelrivera1855.gmail.com> wrote:
>
> > I apologize for not mention I was running antechber. Thanks for your
> > input! Do you think it is wise to remove all H from my ligands? I am
> > not sure if antechamber recognizes Implicate hydrogen placements . I
> > am also positive tat my partials are all zero since the last row in
> > the files are all 0. Thanks again!
> > On Nov 9, 2016 1:22 AM, "Hannes Loeffler" <Hannes.Loeffler.stfc.ac.uk>
> > wrote:
> >
> > > On Tue, 8 Nov 2016 13:50:23 -0700
> > > Miguel Rivera <miguelrivera1855.gmail.com> wrote:
> > >
> > > > Hello all
> > > > I am still new at this so please bear with me.
> > > >
> > > > I am having some problems running the beginning of the FEW
> > > > calculations. I have set up my ligands to have all partial
> > > > charges to be 0.0000
> > >
> > > Why would you want to do that? Because you are running
> > > antechamber...
> > >
> > >
> > > > Info: Bond types are assigned for valence state 22 with penalty
> > > > of 1 Total number of electrons: 697; net charge: 0
> > > > INFO: Number of electrons is odd: 697
> > > > Please check the total charge (-nc flag) and spin
> > > > multiplicity (-m flag)
> > > > Running: /opt/apps/intel15/mvapich2_2_1/amber/14.0/bin/sqm -O -i
> > > > sqm.in -o sqm.out
> > > > Error: cannot run
> > > > "/opt/apps/intel15/mvapich2_2_1/amber/14.0/bin/sqm -O -i sqm.in
> > > > -o sqm.out" of bcc() in charge.c properly, exit
> > >
> > > ... to compute partial charges but it tells you that your molecule
> > > does not have zero charge or you are missing/having too much atoms.
> > >
> > >
> > > Cheers,
> > > Hannes.
> > >
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Received on Wed Nov 09 2016 - 01:00:02 PST
