in this case I would strongly suggest generating new parameters for these
molecules, I don't think manual tweaking will get you anything very
accurate. again it depends on your goals and what sort of accuracy you need
in this model.
On Thu, Sep 17, 2015 at 1:35 PM, Hector A. Baldoni <hbaldoni.unsl.edu.ar>
wrote:
> Dear professors,
>
> Thank you very much for all the feedback. Like it was said deletebond
> would be a very helpful feature to my goal. I have one more question:
> suppose that after delete the desired bond length, a charge redistribution
> of -q over the target enzyme atom and +q over the target ligand atom is
> desired. it would be also possible to do it by ParmEd.
>
> Best whishes,
> Hector.
>
>
> > thanks, that's a very helpful feature. of course people should think
> about
> > whether the remaining terms are still reasonable since it's a different
> > molecule now. for example, should the atom types or partial charges
> > change?
> > I can imagine lots of cases where deleting a bond would be useful, but
> > other cases where people should probably generate a new prmtop from
> > scratch, depending on exactly what they are trying to learn. just adding
> > that here in case people read the archives...
> >
> > On Thu, Sep 17, 2015 at 11:16 AM, Jason Swails <jason.swails.gmail.com>
> > wrote:
> >
> >> On Thu, Sep 17, 2015 at 9:48 AM, Carlos Simmerling <
> >> carlos.simmerling.gmail.com> wrote:
> >>
> >> > Jason - correct me if I'm wrong, but if you delete the bond parameter,
> >> it's
> >> > true that it won't be there, but it won't delete the angle term
> >> between
> >> > atoms across the previous bond, or the torsion parameters. There is
> >> also
> >> > the problem of the nonbonded interactions. the atoms previously bonded
> >> > won't have any nonbonded, nor will the 1-3 atoms, so these molecules
> >> can
> >> > float on top of each other near the deleted bond. I would imagine the
> >> only
> >> > good way to do this is to remove the bond before you make the prmtop,
> >> not
> >> > after... unless parmed is smarter than I thought!
> >> >
> >>
> >> ​ParmEd is smarter than you thought ;). deleteBond does all of this.
> >> It
> >> deletes the bond in its entirety (including all other valence terms that
> >> include that bond), and it always recomputes the exclusions before
> >> writing
> >> a topology file.
> >>
> >> All the best,
> >> Jason
> >>
> >> --
> >> Jason M. Swails
> >> BioMaPS,
> >> Rutgers University
> >> Postdoctoral Researcher
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>
>
> --------------------------------------
> Dr. Héctor A. Baldoni
> Profesor Adjunto
> Departamento de Química
> Área de Química General e Inorgánica
> Universidad Nacional de San Luis
> Chacabuco 917 (D5700BWS)
> San Luis - Argentina
> hbaldoni at unsl dot edu dot ar
> Tel.:+54-(0)266-4520300 ext. 6157
> --------------------------------------
>
>
>
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Received on Thu Sep 17 2015 - 11:30:04 PDT
