On Wed, Oct 28, 2015 at 7:27 AM, Alan <alanwilter.gmail.com> wrote:
> I found that now CHAMBER is part of ParmEd. Yet, still looking for a way to
> generate Amber parm files with Charmm content.
>
​The best way to do that is going to be with ParmEd -- this has gotten
especially easier in recent versions on Github.
The core data structure there -- called `Structure` -- that represents a
FF-parametrized system has attributes with the various parameters and
types. Once you instantiate one of those classes (or any subclass, like
the GromacsTopologyFile or CharmmPsfFile), you can call instance.save("​
something.parm7") and it will automatically convert to the Amber topology
file format and save the file.
If it has CHARMM-specific parameter types (namely arbitrary 1-4 L-J
parameters, Urey-Bradley terms, or harmonic impropers), then the generated
topology file will be the chamber-style.
So for converting from a GROMACS topology specifying the CHARMM force field
to an Amber prmtop is as simple as:
import parmed as pmd
pmd.load_file('gromacs.top').save('amber.parm7')
Or converting the other way around:
import parmed as pmd
pmd.load_file('amber.parm7').save('gromacs.top')
:). Inside the parmed interpreter, the only conversions supported are
those *to* the Amber force field (the chamber and gromber actions).
HTH,
Jason
​
​
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Oct 28 2015 - 07:30:03 PDT
