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
>
>
> _______________________________________________
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>
--
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 Tue Jun 12 2018 - 14:00:01 PDT
