Re: [AMBER-Developers] [AMBER] ATOMIC NUMBER section in prmtop file - Sustiva example

From: James Maier <>
Date: Fri, 31 Jan 2014 22:19:04 -0500

On Fri, Jan 31, 2014 at 4:27 PM, David A Case <>wrote:

> > The mol2 file format does not specify element information.
> Yes and no: the atom type ("cl" in this case) is enough to determine both
> the
> mass and the atomic number. If LEaP is getting either one wrong, that's a
> bug
> that should be fixed.

Agreed. I just made a branch AtomicNumberAtomTypes that interested parties
can look at...

I thought it made most sense to add atomic number to the MASS section of
parameter library files, since mass, polarizability, and other info can be
specified there already, and since mol2 implies element by the atom type
that starts each line anyway.

I added the possibility of a fifth column in this first section (there were
four before), the fifth being atomic number. It is optional, as the fourth
column (a screen parameter).

If the element is specified there, it will override any other leap
elemental determinations. If it's absent, the behavior will proceed as

I've updated gaff.dat for the cl atom type:

cl 35.45 1.910 0.0 17 Chlorine

Note the 2 extra columns. (The fourth column defaults to 0.0 anyway if

I've verified that this results in ATOMIC_NUMBER of 17 for the tutorial at and also tested some
peptides to make sure they did not change.

Clearly, however, more testing is needed (along with test cases, I'm sure).

If anyone thinks this could be useful, help testing it would be
appreciated. And I'm sure other atom types could have this info added, as

In the meantime, it's safe in its own little branch.

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Received on Fri Jan 31 2014 - 19:30:03 PST
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