Thank so much Mathias,
I think your way to calculate the number of ions to add is much easier.
Please correct me if I am wrong for my calculations below:
I have protein+RNA+ligand with charge -11.00.
The number of water added is 20500 residues.
I want salt concentration 0.15 M. Using your formula,
I have to add 50 Na+ and 61 Cl- ions.
The second thing, I will set up my system with the following steps:
sol=loadpdb complex.pdb
solvatebox sol TIP3PBOX 10.0
addionsrand sol Na+ 50
addionsrand sol Cl- 61
charge sol
addions Na+ 0
saveamberparm .top .crd
Please correct me if I am wrong.
Thanks in advance.
best regards,
nadaafiva
Pada tanggal Kam, 2 Jul 2020 pukul 20.18 Matias Machado <
mmachado.pasteur.edu.uy> menulis:
> Dear Nada Afiva,
>
> This question is answered in the following threads:
>
> http://archive.ambermd.org/202002/0194.html
> http://archive.ambermd.org/202003/0040.html
>
> I do NOT recommend the strategy of neutralizing then adding salt, this
> leads to overestimation of the macroscopic salt.
>
> The best way to estimate the volume of the solvent is using the number of
> water molecules.
>
> Best,
>
> Matias
>
> ------------------------------------
> PhD.
> Researcher at Biomolecular Simulations Lab.
> Institut Pasteur de Montevideo | Uruguay
> [http://pasteur.uy/en/labs/biomolecular-simulations-laboratory]
> [http://www.sirahff.com]
>
> ----- Mensaje original -----
> De: "Nada Afiva" <nadaafiva.gmail.com>
> Para: "AMBER Mailing List" <amber.ambermd.org>
> Enviados: Jueves, 2 de Julio 2020 5:34:28
> Asunto: Re: [AMBER] How to set salt concentration
>
> Thanks so much for your helps.
> I really appreciate it.
>
> Best,
> nadaafiva
>
> Pada tanggal Kam, 2 Jul 2020 pukul 11.15 Aashish Bhatt <
> aashish.ph16221.inst.ac.in> menulis:
>
> > Dear Nada
> >
> > Please look at the link
> > https://www.phys.ksu.edu/personal/schmit/SLTCAP/SLTCAP.html
> >
> > Best Regards
> >
> > Aashish
> >
> >
> > On Thu, Jul 2, 2020 at 9:41 AM Suchetana Gupta <tutulg.gmail.com> wrote:
> >
> > > You can first set the charge of the system to zero, in Leap by the
> usual
> > > method. And then follow the same commands to add the required number of
> > > ions to attain the desired concentration.
> > > There is an old thread in this forum regarding this. Please look for it
> > for
> > > details.
> > > Thanks
> > > Suchetana
> > >
> > > On Thu, 2 Jul 2020, 09:25 Nada Afiva, <nadaafiva.gmail.com> wrote:
> > >
> > > > Dear all,
> > > > I would like to simulate receptor-ligand complex and set the salt
> > > > concentration 0.1 M.
> > > > If anyone knows how to set the concentration, please let me know.
> > > > Thank you.
> > > >
> > > > Nada afiva
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Received on Fri Jul 03 2020 - 03:00:04 PDT
