Hi,
For topology conversion, it would be best to use ParmEd to do that
Jason made an example here:
https://github.com/ParmEd/ParmEd/issues/631 (required
develop version of ParmEd)
Just curious: what type of analysis that AMBER does not offer (so we can
add more function if possible).
Hai
import parmed as pmd
amber = pmd.load_file('prmtop', 'inpcrd')
# Save a GROMACS topology and GRO file
amber.save('gromacs.top')
amber.save('gromacs.gro')
On Thu, Mar 10, 2016 at 3:55 PM, Robert Molt <rwmolt07.gmail.com> wrote:
> Good afternoon,
>
> I would like to convert my data into the GROMACS file type because I
> need to use an analysis tool only written for GROMACS. It's easy enough
> to convert a trajectory file in cpptraj:
>
> parm piggy.prmtop
> trajin full_no_waters.mdcrd 1 last 1
> autoimage
> trajout gromacs.trr trr
> go
> quit
>
> It does not seem, from the options in the manual, that cpptraj has a way
> to produce an associated parameter file in the GROMACS format. This
> confuses me, because I am unsure what good a GROMACS trajectory would be
> without the associated topology file. Under parmwrite, the manual seems
> to imply that one can select an alternative format for the parameter
> file (but the manual gives no examples of what formats are possible). Is
> it possible to convert Amber topology files to GROMACS style using the
> parmwrite keyword in cpptraj?
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 10 2016 - 13:30:03 PST
