Re: [AMBER] ParmEd

From: Neha Gandhi <n.gandhiau.gmail.com>
Date: Tue, 5 Jul 2016 13:37:26 +1000

Thanks Jason and Daniel.

I could easily convert the files in test files in ParmEd. However, I have
trouble converting gromacs topology file (protein and ions assigned opls
force field) with gromber. Opls atomtypes are also problematic to convert
using acpype.
I thought of using opls parm files included in AMBER package but they don't
have compatible opls parameters for tip4p water and ions.

Regards,
Neha


On 5 July 2016 at 12:30, Jason Swails <jason.swails.gmail.com> wrote:

> On Mon, Jul 4, 2016 at 10:09 PM, Neha Gandhi <n.gandhiau.gmail.com> wrote:
>
> > Thanks Jason,
> >
> > Is there a manual for ParmEd commands?
> > I ran the gromber command successfully however I don't see any output
> files
> > in the directory. :(
> >
>
> ‚ÄčThe gromber action in itself does not actually output any files. It reads
> in a GROMACS topology and coordinate file (GRO, PDB, ..., any supported
> file format that has coordinates) and converts them into its internal Amber
> representation.
>
> To write a prmtop and inpcrd file, you need to use the "outparm" command.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
Regards,
Dr. Neha S. Gandhi,
Vice Chancellor's Research Fellow,
Queensland University of Technology,
2 George Street, Brisbane, QLD 4000
Australia
LinkedIn
Research Gate
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jul 04 2016 - 21:00:02 PDT
Custom Search