Re: [AMBER-Developers] Proposed parm top addition

From: Jason Swails <>
Date: Thu, 2 Feb 2012 13:28:51 -0500

On Thu, Feb 2, 2012 at 12:18 PM, David A Case <>wrote:

> On Thu, Feb 02, 2012, Jason Swails wrote:
> >
> >
> > Alternatively I could add a command in parmed to add the atomic
> > number section so people can easily adapt their prmtops to the new
> > standard. That would make it less painful to make Amber 12 backwards
> > incompatible.
> Sounds good to me....dac

Easy enough to do. I had just assigned extra points and lone pairs (EP) an
atomic number of 0. It seems to me to be the only logical choice. Yes?
 The rest were chosen to minimize mass differences (so this would only be
an issue if people artificially bumped their masses up to something
significantly different -- it'll still work with almost every isotope of
any atom).

James -- is that what you guys had decided to do for EPs also? Or had you
not thought about it? (I'm not sure how LEaP treats them internally).

All the best,

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Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER-Developers mailing list
Received on Thu Feb 02 2012 - 10:30:03 PST
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