Re: Generating PSF from modified AMBER ff

From: Seth Lilavivat (sethl_at_gatech.edu)
Date: Wed Mar 19 2008 - 12:53:27 CDT

Really? Because when you run NAMDEnergy you must select a structure/psf
file. If you do not, then it gives you an error saying that you need to have
psf file, "Error: no structure (psf) file found!"

Seth

On 3/19/08, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
>
> Why do you need to generate a psf for this? namdenergy should work fine
> with AMBER files...
> Peter
>
> Seth Lilavivat wrote:
> > Dear NAMD community,
> >
> > I have been using NAMD with an AMBER force field which has
> > modifications to accomidate modified nucleic acids and a novel ligand.
> > I would like to use NAMD energy to for my energy calculations which
> > means that I need to generate a .psf file. This seems challenging.
> > Would I have to make modifications to the CHARMM topology file in
> > order to create a PSF or is there another way to do it?
> >
> > Thanks,
> > Seth Lilavivat
> > Georgia Institute of Technology
>

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