Re: [AMBER-Developers] [AMBER] Group defining heavy atoms

From: Hannes Loeffler <>
Date: Mon, 26 Jan 2015 11:00:31 +0000

On Thu, 22 Jan 2015 10:48:47 -0500
Jason Swails <> wrote:

> Something like VMD’s or PyMol’s selection syntax would indeed be
> nice. I suspect it will be both time-consuming and somewhat
> difficult, though (I watched someone implement it in a Python
> package, but they made extensive use of a high-level library for
> parsing and interpreting the selection strings, which we wouldn’t
> have available in Fortran).

I think what I had in mind is pre-computed masks. Leap does, in
principle, "know" what it is dealing with because eventually it is all
based on residue names (there is a set of residue names for proteins,
another for DNA/RNA, etc). The task for leap (but there is apparently
no mechanism for this yet) or ParmEd would then be to appropriately tag
molecule types in the prmtop file. This could also be used by a user
to shorten overly long masks.

> > This reminds me, what ever happened to the proposal some years back
> > to retain certain information from the PDB like chain IDs and
> > original residue numbers in the prmtop?
> That was offloaded to a separate program (add_pdb).

Ok, many thanks.


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Received on Mon Jan 26 2015 - 03:30:03 PST
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