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.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.cerm.unifi.it wrote:
> From: mori.cerm.unifi.it
> Subject: Re: AMBER: ligand unit charge is not zero
> To: amber.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
> >
> >
> > Send instant messages to your online friends
> http://uk.messenger.yahoo.com
> >
> -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber.scripps.edu
> > To unsubscribe, send "unsubscribe amber" (in
> the *body* of the email)
> > to majordomo.scripps.edu
> >
> >
> > __________ Informazione NOD32 3142 (20080528)
> __________
> >
> > Questo messaggio � stato controllato dal Sistema
> Antivirus NOD32
> > http://www.nod32.it
> >
> >
> >
> >
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the
> *body* of the email)
> to majordomo.scripps.edu
Send instant messages to your online friends
http://uk.messenger.yahoo.com
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Sun Jun 01 2008 - 06:07:30 PDT
