The answer is "yes, it *should* work". But check it carefully to ensure
you get the same results as just using the Amber files directly.
ParmEd will convert to a PSF file (and write the parameters to CHARMM
format), but I'm unsure if NAMD can read the special prm file directives
that CHARMM uses to indicate it's the AMBER force field functional form
instead of CHARMM's.
HTH,
Jason
On Tue, Jun 12, 2018 at 4:33 PM, Stefano Guglielmo <
stefano.guglielmo.unito.it> wrote:
> Dear Pengfei,
> thanks for your message.
> My question is related to the following issue: I have generated the
> topoplogy of a system made by protein, ligand, membrane and water box using
> ambertools (obviously fed with the appropriate amber ff's), but I would
> like to use NAMD as MD engine; I ran the simulation properly using the NAMD
> option "amber on" and amber topology provided by amber tools; I was
> wondering if, after generating psf from amber topology with parmed, the psf
> file can be used with NAMD coupled with a charmm ff (and which one) or
> still with the option "amber on" or neither of two. The reason for all this
> mess? Amber tools gave me a more reliable parameterization for the ligand,
> but using NAMD and VMD with the psf I could use more selection options for
> analysis.
>
> I hope I didn't bore you
> thanks
> Stefano
>
> 2018-06-12 22:02 GMT+02:00 Pengfei Li <ambermailpengfei.gmail.com>:
>
> > Dear Stefano,
> >
> > CHARMM can mean a force field or a software package. Please clarify your
> > question.
> >
> > You want to build psf file with CHARMM force field for using in the
> CHARMM
> > software package? If so, there is no need to use parmed, because this
> will
> > be redundant, the straightforward way is to build this psf file though
> > using CHARMM.
> >
> > What I understand is that you want to build a psf file using the AMBER
> > force field through parmed software and the AMBER topology and coordinate
> > files, and then use the psf file in the CHARMM software package for
> > simulations. Is that right?
> >
> > -Pengfei
> >
> > > On Jun 7, 2018, at 7:56 PM, Stefano Guglielmo <
> > stefano.guglielmo.unito.it> wrote:
> > >
> > > Dear amber users,
> > >
> > > I would like to know if a psf file generated with parmed from a prmtop
> > file
> > > can be used for a simulation with charmm force field (for example in
> > CHARMM
> > > or NAMD) and, if this is the case, with which among the charmm force
> > fields.
> > >
> > > Thanks in advance
> > > Stefano
> > >
> > > --
> > > Stefano GUGLIELMO PhD
> > > Assistant Professor of Medicinal Chemistry
> > > Department of Drug Science and Technology
> > > Via P. Giuria 9
> > > 10125 Turin, ITALY
> > > ph. +39 (0)11 6707178
> > > _______________________________________________
> > > 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
> >
>
>
>
> --
> Stefano GUGLIELMO PhD
> Assistant Professor of Medicinal Chemistry
> Department of Drug Science and Technology
> Via P. Giuria 9
> 10125 Turin, ITALY
> ph. +39 (0)11 6707178
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 13 2018 - 20:00:03 PDT
