Re: [AMBER] Strange TIP3P solvent box distortions in Amber 18 with Mg2+, but no MG

From: David Case <>
Date: Fri, 7 Dec 2018 03:02:59 +0000

On Thu, Dec 06, 2018, Kasprzak, Wojciech (NIH/NCI) [C] wrote:

> the tutorial "addIons mol Mg2+ 0" yielded an error.

Can you (re-) say which tutorial this is, so we can fix it?

The PDB has standard names for common ions, and "MG" is the name chosen
for Mg2+. In the bad (not-so-) old days, Amber developers (along with
those in other simulation communities) did not pay much attention to
such standards, and just made up whatever names they liked or thought
were appropriate.

Such mistakes can be hard to fix, since there is a competing desire that
programs continue to give the same results for old inputs, even when those
inputs are outdated. We partially succumbed to this in Amber by defining
"Na+", "K+" and "Cl-" (all non-standard) as aliases for the standard names
NA, K and CL. We did not do the same for Mg2+, hence the errors that you
are seeing.

Two take-home points:

1. People should use NA, K, CL, MG, (etc) as the names for monatomic
ions. See $AMBERHOME/dat/leap/lib/atomic_ions.lib for the the ones we
provide in our standard libraries.

2. And you should indeed carry out solvent equilibrations under NPT
conditions, for the reasons that Dave Cerutti outlined.


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Received on Thu Dec 06 2018 - 19:30:03 PST
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