Thanks a lot for your comments. When I minimize the structure, the results are even worst than after MD simulation. Extending the simulation the angle gets better, although not perfect. Maybe it´s the best MM can do for the moment!
Best wishes,
Rebeca.
> Date: Thu, 12 Feb 2015 07:27:32 -0500
> From: case.biomaps.rutgers.edu
> To: amber.ambermd.org
> Subject: Re: [AMBER] alkynes in GAFF
>
> On Thu, Feb 12, 2015, Rebeca García Fandiño wrote:
>
> > I am trying to simulate an organic molecule containing an alkyne, using
> > GROMACS and the GAFF force field.
> >
> > The resulting structure from MD simulations is not correct, since the
> > triple bonds should be linear (C-C=C-H), and I observe an angle among
> > the atoms involved.
>
> What is the angle you see? What angle do you get if you minimize the
> structure? Linear molecules can be difficult for molecular mechanics force
> fields, since the angle force becomes poorly defined near 180 degrees.
>
> ...dac
>
>
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Received on Thu Feb 12 2015 - 05:00:02 PST
