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

From: David A Case <>
Date: Fri, 31 Jan 2014 16:27:22 -0500

> On Fri, Jan 31, 2014 at 1:29 PM, rohitarora10 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?

It's a bug, as far as I can tell.
> 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. The ATOMIC_NUMBER section is relatively recent, so we
need to make sure that this bug is fixed. LEaP knows that the element is
"Cl" -- this needs to be correctly translated into the correct atomic number.

[The sustiva test case has commented out the check of the prmtop file that is
created, which is one reason we didn't see this before now.]

> 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).

This is, of course, prudent, but we (as developers) need to get this fixed.
Thanks for the report.


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Received on Fri Jan 31 2014 - 13:30:02 PST
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