thanks for your answer, in detail the problem that I have is that I have been running production MD simulation of enzyme with a ligand by Amber14 with ff14sb force field for the protein and Gaff for the ligand, in periodic water box, but amidic bond or peptide bond (CO-NH) of the ligand rotates during the dynamics, I would like to know how can I solution this problem because in the manual user doesn t explain about restraints for the ligand, like its my case.
I attched the structure of the ligand.
Any suggestions?
Thanks
________________________________
De: Carlos Simmerling <carlos.simmerling.gmail.com>
Enviado: viernes, 13 de julio de 2018 15:30:54
Para: AMBER Mailing List
Asunto: Re: [AMBER] peptide bond restraints
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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
- application/vnd.palm attachment: lig.pdb
Received on Wed Jul 18 2018 - 15:00:02 PDT
