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

From: Jason Swails <>
Date: Thu, 22 Jan 2015 08:45:41 -0500

> 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 :).

All the best,

[1] As an aside, I had originally written a free-format input file spec for multi-D REMD several years ago (that I rather liked, and was proud of for getting it to work correctly in the Fortran-MPI program I wrote it for :). But there was significant resistance to that approach, and I was asked to recast the input in Fortran namelist-form.

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Jan 22 2015 - 06:00:06 PST
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