It sounds like maybe something isn't right about the gaff setup for your
ligand. It might help to post a question about applying gaff to your
ligand, explaining the functional groups and what happens. I think it's
very unlikely that this is related to ff14SB.
On Fri, Jul 13, 2018, 2:23 PM lucrecia bogado <lucre686.hotmail.com> wrote:
> for the ligand I have used the force field GAFF, with RESP charges.
>
> thanks
>
> ________________________________
> De: Carlos Simmerling <carlos.simmerling.gmail.com>
> Enviado: jueves, 12 de julio de 2018 20:08:22
> Para: AMBER Mailing List
> Asunto: Re: [AMBER] peptide bond restraints
>
> Ff14SB doesn't have ligand parameters - did you load a modified force field
> for a ligand? Or is the ligand a standard peptide? If not I suspect it is
> something in how the ligand was set up.
>
> On Thu, Jul 12, 2018, 6:19 PM lucrecia bogado <lucre686.hotmail.com>
> wrote:
>
> > Amber List members,
> >
> > I'm new to Amber handling and I'm trying to solve a problem:
> >
> > I have been running production MD simulation of enzyme with a ligand by
> > Amber14 with ff14sb force field in periodic water box, but amidic bond
> or
> > peptide bond (CO-NH) of the ligand rotates during the dynamics
> >
> > I would like to know what restrictions should be placed to avoid this
> > rotation or where to look for such specifications, because in the user's
> > manual they are not very clear.
> >
> > I would appreciate your help.
> >
> >
> > Thank you,
> >
> > Lucrecia
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> >
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Received on Fri Jul 13 2018 - 12:00:04 PDT
