Re: psf from parmed

From: Stefano Guglielmo (stefano.guglielmo_at_unito.it)
Date: Fri Jun 08 2018 - 09:20:59 CDT

Thanks for quick reply.
Do you think it is worth trying to run namd using the parmed psf (generated
with amber ff) as structure file and the option "amber on", or I can take
for granted that it is not going to work?

Thanks again

2018-06-08 16:03 GMT+02:00 Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>:

> ParmEd can in principle do both, depending on the force field it was fed
> with. Amber and CHARMM atomtypes don't always coincide, so I'd be curious
> as to how ParmEd would do the translation. My understanding is that it will
> take the parameter and topologies from the original prmtop file and
> translate the filetypes involved, but not change the force fields from
> whatever was fed in. So if your original prmtop file used CHARMM
> parameters, you are all set, but otherwise I think you might need an
> alternative approach, such as rebuilding the system with psfgen or CHARMM.
>
> -Josh
>
>
>
> On 2018-06-08 07:15:31-06:00 owner-namd-l_at_ks.uiuc.edu wrote:
>
> Dear namd 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 in NAMD or if it
> is meant to be used with the "amber on" option.
> 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
>
>

-- 
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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