Re: [AMBER] Recover the water model and periodic box from built parm files

From: Jason Swails <>
Date: Mon, 22 Jun 2015 16:52:46 -0400

On Mon, Jun 22, 2015 at 4:34 PM, Brian Radak <>

> Ah, no, I'm not sure - that's just how I recall doing things from a few
> years back. I can only say that I know that /that/ worked and it wasn't
> too much of an ordeal to get going. It's very possible that an older and
> wiser Brian would find things are a bit more simple.

​From a functional perspective, TER cards are only needed by LEaP to
*prevent* adjacent residues from being linked. The only time LEaP ever
does this is when that residue has a HEAD or TAIL defined (which it
obviously doesn't for water).

So it's necessary between protein or nucleic acid chains, but not after
isolated molecules. As with Dave, I've never had problems using
ambpdb-generated files directly with tleap.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Mon Jun 22 2015 - 14:00:04 PDT
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