AMBER Archive (2004)

Subject: Re: AMBER: How to add H+ ion in leap?

From: Bill Ross (
Date: Tue Feb 17 2004 - 15:09:01 CST

> So what type you will choose?

I would either choose some other H type at random (it likely
won't matter), or use Li+. To be procedurally accurate I would
create my own type by using experimental data from neutron
scattering if available, plugging the first radial distribution
peak of H+ and water O into the vdw parameter equation derived
in Ross and Hardin (JACS 116, 6070 (1994)) to get R* for epsilon
of .1, then verify the 1st peak in a simulation with water.

> Aslo, I tried to add a H+ ion by add 3 lines in pdb:
> ATOM 1232 H+ H+ 77 45.303 29.749 7.497 1.00 0.00
> But after I load this pdb and check the charge, it's still 0.

The charge comes from the residue definition. You would need
to define a H+ residue, see amber7/dat/leap/lib/ions94.cmd.

> While a line
> ATOM 1232 Li+ Li+ 77 45.303 29.749 7.497 1.00 0.00
> can change the total charge to +1.

Try setting it to 2 - the charge will remain 1.

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