Hi Hai, :D
My question is:
I want to add ions to my systems which are
1) uniformly distributed in the waterbox and s
2) hould be away from the solute (protein of interest)
Thanks,
Hirdesh
On Tue, Dec 20, 2016 at 12:19 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> hi, so what's your specific question here? :D
>
> Hai
>
> On Tue, Dec 20, 2016 at 1:15 PM, Hirdesh Kumar <hirdesh.iitd.gmail.com>
> wrote:
>
> > Hi,
> >
> > My system consists of a protein-ligand complex with few co-crystallized
> > waters and I am trying to add ions to this system.
> >
> > I am using AmberTool16. First I solvated my system and next when I tried
> > 1) addIonsRand: I found that ions were random distributed but some of the
> > ions were within my protein. Therefore, I can not use such system.
> >
> > 2) addions2: I found that all ions were outside the water box and were
> > arranged in one plane. I understand that "addions2" considers solute and
> > solvent both and therefore added ions were outside the box.
> >
> > 3) addions: This time I found that ions were within the solvent box and
> > were not inside the protein. But, the ions are still not uniformly
> > distributed (see attached figure). I am afraid if it may affect my
> > simulation.
> >
> >
> >
> >
> > *Thanks,Hirdesh*
> >
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> >
> >
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Received on Tue Dec 20 2016 - 10:30:04 PST
