Thanks for the details, I will give it a try asap.
Stefano
2018-06-14 4:38 GMT+02:00 Jason Swails <jason.swails.gmail.com>:
> 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
> > > > _______________________________________________
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> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > >
> > > _______________________________________________
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> > > 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
> _______________________________________________
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> 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
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Received on Thu Jun 14 2018 - 00:00:02 PDT
