On Tue, Dec 8, 2015 at 11:12 AM, Nathalie Willems <
nathalie.willems.bioch.ox.ac.uk> wrote:
> Dear Jason,
>
> Thanks for the clear and quick answer - this makes sense now. Is there
> therefore a way of outputting the dihedrals combinations defined by the
> protein topology in a single line format in AMBER, such that each one only
> appears once? This is mainly for comparison reasons, as I would like to
> compare how the glycoprotein topology is defined in AMBER to how it is
> defined in a gromacs topology (both using the Amber ff99SB forcefield).
>
No, I there really is not a straightforward way to do that with existing
commands in Amber. But I would recommend checking out the ParmEd Github
project, which has incorporated a lot of work to support Gromacs topology
files and should make such a comparison easier. Check out
http://github.com/ParmEd/ParmEd for more information.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Dec 08 2015 - 12:30:03 PST
