One option I have used in the past as a bit of a hack is to convert them to
gromacs, merge them there and then use gromber to get them back to amber.
On Mon, Feb 18, 2019, 12:51 PM Jason Swails <jason.swails.gmail.com wrote:
> On Sat, Feb 2, 2019 at 12:10 PM Stefano Guglielmo <
> stefano.guglielmo.unito.it> wrote:
>
> > Dear Amber users,
> > is there a way to merge two systems (eg a protein and a ligand) starting
> > from two distinct prmtop files? I have googled a bit, trying to focus on
> > ParmEd utility and it seemed that the combineMolecules command could fit,
> > but I couldn't find the command in the version I have installed (3.0.3).
> > Does anyone have any suggestions?
> >
>
> combineMolecules doesn't do that -- it takes two distinct 'molecules' in
> the system and hacks the topology file to make programs *think* they're
> just one molecule. There aren't many good reasons to do this, though, so I
> removed the command (it was never really used as far as I knew).
>
> The "parmed" program itself can't do this. However, the ParmEd API does
> have a convenient way to combine two systems -- via the + operator. But
> you have to write a short script to do this in Python. Something like the
> following could get you started:
>
> #!/usr/bin/env python
>
> import parmed as pmd
>
> parm1 = pmd.load_file('first_system.parm7', 'first_system.rst7')
> parm2 = pmd.load_file('second_system.parm7', 'second_system.rst7')
> joined = parm1 + parm2
> joined.save('new_system.parm7')
> joined.save('new_system.rst7')
>
> HTH,
> Jason
>
> --
> Jason M. Swails
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Received on Mon Feb 18 2019 - 13:30:02 PST
