Hi,
The addition of ions individually i. e. Na and Cl ions in separate command
can solve also this problem.
On Dec 21, 2016 12:15 AM, "Hirdesh Kumar" <hirdesh.iitd.gmail.com> wrote:
> 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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Received on Wed Dec 21 2016 - 04:30:02 PST
