Re: [AMBER] Number Excluded Atoms List Generation

From: Jason Swails <>
Date: Thu, 7 Mar 2013 13:52:41 -0500

A few comments -- have you looked into ParmEd at all? It has fairly
sophisticated topology file editing capabilities, written in Python (and it
is about as easy as I could make it to extend for your own purposes).
 Furthermore, the code to generate the exclusion list (reproducing exactly
what leap generates, even for extra points) is present there as well

>From personal experience, a topology file editor is a complex thing to
write and can take a long time to work out all of the small issues; the
ParmEd code has a few years of 'practice' under its belt (and it has an
available Python interpreter so you can insert your own Python code to
customize it).

</parmed advertisement>

I've written a document that should serve as a fairly complete prmtop spec
document. I wrote it up as I was developing ParmEd---I've attached an
unpolished form of it.


On Thu, Mar 7, 2013 at 11:53 AM, Browning, Nicholas <> wrote:

> Dear Amber Users/Developers,
> I'm currently writing some code which involves the modification of prmtop
> files generated from leap. I'm interested in knowing how the following list
> is generated, such that I can replicate it in my code.
> I've looked into the leap src and I've found snippets of code involving
> the numex/natex lists, but very little in the way of commentary. Does
> anyone have any insight into this?
> Kind Regards,
> Nick Browning
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate

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Received on Thu Mar 07 2013 - 11:00:03 PST
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