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!
carlos
On Thu, Sep 17, 2015 at 9:44 AM, Hector A. Baldoni <hbaldoni.unsl.edu.ar>
wrote:
> Dear Professor,
>
> Thank you for providing the requested information. If you do not mind
> would you give me an example of how to use the command.
>
>
> Greeting,
> Hector.
>
>
> > On Wed, Sep 16, 2015 at 4:11 PM, Hector A. Baldoni <hbaldoni.unsl.edu.ar
> >
> > wrote:
> >
> >> Dear Amber users,
> >>
> >> It Would be possible to use ParmEd to delete a single bond length its
> >> bond
> >> angles and dihedral parameters from a topology file representing a
> >> covalently bonded Enzyme-substrate complex in order to generate its
> >> Michaelis complex. If it’s possible how I must to proceed. Any clue
> >> will
> >> be wellcome.
> >>
> >
> > ​The command you want is "deleteBond".
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --------------------------------------
> 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
> --------------------------------------
>
>
> _______________________________________________
> 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
Received on Thu Sep 17 2015 - 07:00:06 PDT
