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
Received on Tue Dec 20 2016 - 10:30:05 PST
