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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> AMBER.ambermd.org
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>
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Received on Fri Jul 13 2018 - 11:30:02 PDT
