On Wed, Jun 21, 2017 at 12:42 PM, Qinghua Liao <scorpio.liao.gmail.com>
wrote:
> Hello,
>
> I used parmed to convert a psf file to a gromacs top file successfully,
> but most of the parameters (LJ, bonded)
> are missing in the top file. How could I use parmed to include the
> parameters for the top file, taking the parameters
> from the force field library file? Thanks a lot!
>
You need to load the parameters from the CHARMM RTF and PRM files first.
So do something like this:
import parmed as pmd
psf = pmd.load_file('your-file.psf')
psf.load_parameters(pmd.charmm.CharmmParameterSet('topology.rtf',
'parameters.prm', ...))
psf.save('gromacs.top')
And that should do it. Obviously you need to change the arguments to
load_file and CharmmParameterSet to reflect your files.
HTH,
Jason
--
Jason M. Swails
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Received on Sun Jun 25 2017 - 12:30:03 PDT
