AMBER Archive (2008)

Subject: Re: AMBER: ligand unit charge is not zero

From: Swarup Gupta (swarupgupta_at_yahoo.com)
Date: Thu May 29 2008 - 07:48:13 CDT

Counterions are added to the system to neutralize the charge of the overall system. The system may contain the protin+ligand.
   
  I would suggest you to read some materials to begin with MD.

amor san juan <amor_sanjuan_at_yahoo.com> wrote:
  Hi,

Thank you for your suggestion. I am a new user of AMBER and I just want to ask a quick question:

In principle, adding counterions to ligand would not give an artifact to the results? I know that counterions are being added to protein when required but to ligands, I am not sure.

Amor

--- On Thu, 29/5/08, mori_at_cerm.unifi.it wrote:

> From: mori_at_cerm.unifi.it
> Subject: Re: AMBER: ligand unit charge is not zero
> To: amber_at_scripps.edu
> Date: Thursday, 29 May, 2008, 5:17 PM
> You can balance the negative charge of your nucleotide by
> the addions or
> addions2 in tleap.
>
>
> amor san juan ha scritto:
> > Hi,
> >
> > I use antechamber in tleap to generate the topology
> and coordinate for a ligand which is a nucleotide (Formula:
> C12H20N4O14P3). The warning is that the charge is equal to
> -3.0. Can anyone give an idea how to solve this warning?
> >
> > --------------------
> > Checking Unit.
> > WARNING: The unperturbed charge of the unit: -2.999980
> is not zero.
> >
> > -- ignoring the warning.
> >
> > Building topology.
> > Building atom parameters.
> > Building bond parameters.
> > Building angle parameters.
> > Building proper torsion parameters.
> > Building improper torsion parameters.
> > old PREP-specified impropers:
> > total 0 improper torsions applied
> > 0 improper torsions in old prep form
> > Building H-Bond parameters.
> > Not Marking per-residue atom chain types.
> > Marking per-residue atom chain types.
> > (no restraints)
> >
> >> edit MGO
> >>
> > Unit Editor: > charge MGO
> > Unit Editor: Total unperturbed charge: -3.0000
> > Unit Editor: Total perturbed charge: -3.0000
> >
> >> quit
> >>
> > --------------------------
> >
> >
> >
> > Thanks,
> > Amor A. San Juan
> >
> >
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