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

From: Alechania Misturini <>
Date: Tue, 3 Jul 2018 10:28:26 -0300

Well, what I tried to say is that, if I run tleap starting with the mol2
and frcmod that I showed in the previous email, just for saving topology
and coordinate, and do this again, but trying to impose this angle
(hc--J3--SI in atom types, H6--CJ3--SI in atom names), the structure
generated is iqual the first one (without impose).
Even trying to change the degree of this imposed angle, the impose option
is ignored, and final structures are always the same.
This behavior happend with this specific angle in this molecule, and with
other 2 molecules the impose didn't work, in another angle and one dihedral

Well, the impose works with atoms names, so, I would think it's well
defined what angle I'm referring to.
Because I need to generate a great number of structures, changing angles in
a range, make too dispendious making it by hand, using an program with
visual interface.
I'll need to find other ways to define angles and torsions. Cause my
problems to fit (with paramfit) these molecules parameters are in the
sampling - generation of this conformers.

I tryed to change the names of atoms, just to find if the problem is with
them, but same results were obtained.

2018-07-03 10:00 GMT-03:00 David A Case <>:

> 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.
> ....dac
> _______________________________________________
> AMBER mailing list

Alechania Misturini
Mestranda em Físico-Química
Bacharel e Licenciada em Química
Grupo de Estrutura Eletrônica Molecular –〈
*Departamento de Química – CFM*
*Universidade Federal de Santa Catarina – Brasil*
AMBER mailing list
Received on Tue Jul 03 2018 - 06:30:03 PDT
Custom Search