GM
On Wed, Dec 21, 2016 at 6:12 AM, Prajwal Nandekar <prajwal.pharm07.gmail.com
> wrote:
> 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*
> > > > > >
> > > > > > _______________________________________________
> > > > > > AMBER mailing list
> > > > > > AMBER.ambermd.org
> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >
> > > > > >
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Dec 21 2016 - 08:00:02 PST
