AMBER Archive (2003)

Subject: Re: Simulation under physiological conditions

From: Michal Otyepka (otyepka_at_aix.upol.cz)
Date: Thu May 15 2003 - 10:50:44 CDT

... yes, but the concentration of counterions (Cl-) in my system is only
0.039 M and to reach physiological conditions i have to add about 50 Na+
and Cl- ions, but i dont want to add ions close to protein. What about
modification of WATBOX216 ???

> you may calculate the volume of the solvated box, and obtain the number
> the ions needed to achieve specific salt concentration, say 0.15 M. then
> you want to use leap to add those ions... good luck.. yan
>
>
> > Dear AMBERs,
> >
> > could you recommend me, please, the easiest way to build .top and .crd
> > file in Xleap for simulation with 0.15M - NaCl?
> >
> > Many thanks in advance,
> >
> > Michal Otyepka
> >