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

From: James Maier <>
Date: Fri, 31 Jan 2014 14:33:18 -0500

On Fri, Jan 31, 2014 at 1:29 PM, <> wrote:

> the value in the ATOMIC NUMBER section corresponding to
> CL is 6 (which is atomic number of Carbon), but the MASS is 35.45, which
> is atomic mass of Chlorine.
> Does anyone know why this is happening?

The mol2 file format does not specify element information.

Unfortunately, this makes it difficult for LEaP to determine element
information for some possibly ambiguous atoms, such as those that begin
with c. LEaP determines that the "cl" atom type corresponds with carbon,
giving it atomic number 6.

The atom type "cl", however, is used to give CL its parameters including
mass, as specified by the force field.

Until a general solution is found, I'd recommend caution with non-carbon
elements beginning with c, if you actually need the ATOMIC_NUMBER to be
correct (see below).

> Also, does Amber (sander/pmemd in
> particular) use the ATOMIC NUMBER information during the simulation?

ATOMIC_NUMBER is used to assign GB parameters for the Neck models (e.g.,
igb=8) as well as some GBSA parameters. I think there are plans to use it
for QM calculations within AMBER, as well.

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Received on Fri Jan 31 2014 - 12:00:02 PST
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