On Wed, Jan 3, 2018 at 11:49 AM, Crystal Vander Zanden <
cvanderzanden.unm.edu> wrote:
> Dear AMBER Community,
>
> I am trying to parameterize my system using AMBER force fields, and then do
> molecular dynamics with the GROMACS software. I want to use the Lipid17
> force field, which is not build into GROMACS. Does anyone know of a way to
> do this?
>
You can write a very short Python program to do this using ParmEd. First
thing you need to do is create your prmtop and inpcrd file using tleap.
After that, write a script (let's call it convert.py) to do this.
convert.py will look like this:
import parmed as pmd
parm = pmd.load_file('name-of-your.prmtop', 'name-of-your.inpcrd')
parm.save('gromacs.top')
parm.save('gromacs.gro')
Then run that program using the command
amber.pything convert.py
Then use GROMACS from there.
HTH,
Jason
--
Jason M. Swails
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Received on Fri Jan 05 2018 - 21:30:01 PST
