Re: [AMBER] Strange TIP3P solvent box - reference to the tutorial

From: Kasprzak, Wojciech (NIH/NCI) [C] <"Kasprzak,>
Date: Fri, 7 Dec 2018 13:25:54 +0000

Dr. Case,

Thank you very much for the full explanation of the ion naming conventions.
The tutorial I used as a starting point to setting up my system is at:

An edit and perhaps a comment taken straight from your e-mail would be helpful.

Thank you for all the responses and advice.
Bets regards,
Voytek Kasprzak

Wojciech (Voytek) K. Kasprzak (Contractor)
Bioinformatics Analyst
Basic Science Program
Frederick National Laboratory for Cancer Research
Leidos Biomedical Research, Inc.
Post Office Box B
Frederick, Maryland 21702
Phone: 301-846-5537
From: David Case []
Sent: Thursday, December 6, 2018 10:02 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Strange TIP3P solvent box distortions in Amber 18 with Mg2+, but no MG

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inputs are outdated.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 Fri Dec 07 2018 - 05:30:03 PST
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