Thanks ,
It worked with randomizeions
**
On Tue, Dec 20, 2016 at 12:27 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> May be checking "randomizeions" in cpptraj?
>
> Hai
>
> On Tue, Dec 20, 2016 at 1:25 PM, Hirdesh Kumar <hirdesh.iitd.gmail.com>
> wrote:
>
> > 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 - 11:00:02 PST
