RE: psf from parmed

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Fri Jun 08 2018 - 09:03:43 CDT

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

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