Re: [AMBER] Tleap Impose Doesn't work for defining some angle/diedral

From: David A Case <>
Date: Tue, 3 Jul 2018 09:00:40 -0400

On Tue, Jul 03, 2018, Alechania Misturini wrote:
> I need to vary some angle, for example, so, for this, employ impose
> function of tleap. When I tried to parametrize each parameter, I finded
> errors in three of them, and basically the impose function doesn’t work in
> then.

Can you explain what you mean by "doesn't work"? Also, are you trying
to impose an angle (involving three atoms) or a dihedral/torsion (involving
four atoms)? We're probably going to need an example where we can reproduce
the problem.

That said, the "impose" command in tleap is fragile, since the user is not
asked which atoms to move to make the change: to change a bond length, for
example, should one move the atoms on the "left" side of the bond, those on
the "right", or some combination of the two? This ambiguity can get really
tricky with dihedrals.

The NAB language has routines to set internal coordinates, with arguments that
specify which atoms should move. This (at least to me) has always seemed more
natural. And there are other good molecule building programs outside Amber,
many with good visual interfaces so that you can see immediately what is being
done. Maybe others on the list can offer some good suggestions.


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Received on Tue Jul 03 2018 - 06:30:02 PDT
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