Dear Colleagues!
this is a ligand which I parametrize
http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=ERC&sid=3PDS
I've found it in the leap.log of my ligand
WARNING: The unperturbed charge of the unit: 0.994001 is not zero.
Checking parameters for unit 'ERC'.
Checking for bond parameters.
Checking for angle parameters.
check: Warnings: 1
Unit is OK.
> saveamberparm ERC erc_AC.prmtop erc_AC.inpcrd
Checking Unit.
WARNING: The unperturbed charge of the unit: 0.994001 is not zero.
2013/4/16 Jason Swails <jason.swails.gmail.com>
> On Tue, Apr 16, 2013 at 12:44 AM, James Starlight <jmsstarlight.gmail.com
> >wrote:
>
> > Dear Dr. Case,
> >
> > thank you for your response! The main issue why I've decided to switch
> from
> > sqm is that the topology with not integer charge was producing during
> > parametrization of large ligand (~60 atoms). In my research I deal with
> the
> > horomone-like ligands of membrane receptors. What method of charge
> > computations would be best suitable for the parametrization of such
> > molecules for amber force fields?
> >
>
> When you say 'non-integer', exactly what charge is coming out? Round-off
> errors of 0.0001 to 0.001 are not unusual, and are small enough that you
> can manually adjust the charges on one of the atoms to achieve neutrality.
> sqm and mopac should give roughly the same results (exactly the same if
> they use the same values for the fundamental constants -- I'm not sure
> whether or not this is true).
>
> If the assigned charges result in a significant non-integral charge, the
> problem may lie with antechamber (in which case using mopac won't help),
> and we should get that fixed.
>
> All the best,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Tue Apr 16 2013 - 08:30:03 PDT
