AMBER Archive (2008)

Subject: AMBER: Calculate number of ions

From: Dong Xu (d1xu_at_ucsd.edu)
Date: Sat May 10 2008 - 13:32:01 CDT

Hi All,

I have a question regarding the correct procedure of calculating exact
number of ions needed to reach a certain salt concentration. Say I
want to have 0.15M NaCl in my system and it's already neutralized and
solvated with "solvatebox protein TIP3PBOX 10.0" in tleap. I measure
the water box dimensions in VMD and I calculate the number of ions
based on the volume of the water box. But the problem is that the
number of ions calculated this way is always much larger than the
number of ions calculated from VMD autoionize plug-in. I'm guessing
autoionize plug-in subtracts the volume occupied by the protein? It's
a hassle to use the VMD plug-in because a CHARMM style psf file for
the solvated system is required. So, I was wondering what is the
correct AMBER way of calculating number of ions?

Thanks a lot!

Dong Xu
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