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

From: Hannes Loeffler <>
Date: Thu, 22 Jan 2015 14:16:47 +0000

On Thu, 22 Jan 2015 08:45:41 -0500
Jason Swails <> wrote:

> > On Jan 22, 2015, at 8:33 AM, Gerald Monard
> > <> wrote:
> >
> > Hi,
> >
> > What about reading an external file? It's already the case for
> > distance restraints for example.
> But the distance (and all NMR-related) restraints still take input
> through a namelist, which is subject to the same limitations as I
> mentioned earlier. And I don’t think we need yet another free-format
> input spec. [1]
> I think the solution here is pretty straightforward -- expand the
> character limit and change restraintmask and restraint_wt into
> arrays. That way, backwards compatibility is maintained, and we
> support multiple selection groups through the mask interface. The
> necessary changes should be small, which is the biggest upside :).

Somewhat related, and possibly solving problems likes this but only in
part, would be a feature I always wanted to have for higher flexibility
in defining masks. What I miss is higher level descriptions of e.g.
"proteins" or "nucleotides" or "lipids" or "backbone", etc. Could
probably be simply implemented through additional sections in the
prmtop file.

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? Also, what is the "set ... restype" in
leap used for?


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Received on Thu Jan 22 2015 - 06:30:02 PST
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