Re: [AMBER-Developers] [AMBER] &rst + distance + coordinate restraint

From: Jason Swails <>
Date: Tue, 3 Nov 2015 12:11:05 -0500

Moving this over to the developer's list

On Tue, Nov 3, 2015 at 10:27 AM, Gerald Monard <> wrote:

> OK. I got it now.
> So, now, instead of 'restraint = coordinate(...)', I can do:
> # d2-(d3-d4)
> &rst iat = 11,48, 48, 49, 49, 16,
> rstwt = 1,-1,1, r0 = 3.2, k0 = 0.0, /
> and it works just fine.

​Gerald -- am I correct in reading that this input works while the previous
input with the "natural language" input did not?

If so, that raises a question as to what we should do here. Does anybody
use this input option, and is anybody familiar with the code that can look
into the issues and try to fix the bugs? If not, should we continue to
keep natural language input around when fixes to the problem involve
abandoning it altogether? (Does anybody use it on a regular basis?) Also,
pmemd does not support this input (and likely never will), so these input
files are sander-only.



Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER-Developers mailing list
Received on Tue Nov 03 2015 - 09:30:03 PST
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