RE: psf from parmed

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Fri Jun 08 2018 - 09:30:11 CDT

Hi Stefano,

I *think* "amber on" implies that you use a prmtop and NAMD's ability to read prmtop files, since you can't otherwise give NAMD parameters for your system due to the lack of parameter files. Though I suppose you could also use ParmEd to write out charmm-style parameter files that NAMD will accept. Not knowing exactly what you are doing, I'd recommend either converting properly to CHARMM36 with psfgen, or using NAMD's inbuilt functionality for reading Amber inputs. Anything else is just extra steps to potentially debug when something goes wrong.

-Josh

On 2018-06-08 08:21:03-06:00 Stefano Guglielmo wrote:

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<mailto: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<mailto: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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