Re: [AMBER] Hydrogen Mass Repartitioning without ParmEd

From: Jason Swails <>
Date: Tue, 9 Nov 2021 11:46:31 -0500

On Tue, Nov 9, 2021 at 10:21 AM ABEL Stephane <> wrote:

> Hi Jason,
> >> tleap does not currently support writing a topology file with
> repartitioned masses, and ParmEd is the only option for repartitioning
> within Amber.
> OK
> >> If you describe what you mean by "some reasons", maybe it's
> straightforward
> My aim is to prepare some Amber files for subsequent simulations with
> GROMACS so I have installed a minimal version of AmberTools 21 on an HPC
> machine without python support for using only tleap or Antechamber.
> ParmEd needs some python dependencies (e.g. setuptools, versioneer) and I
> cannot download them to compile the code. That why I asked this question.
> But as there is no other alternative to have the HMR functionality I will
> try to install the full version of Ambertools on a desktop machine to have
> ParmEd works

You can install a copy of Miniconda on the HPC most likely, then conda
install parmed to make it available. The only runtime dependencies that
ParmEd has is numpy (setuptools and versioneer are only needed to build).

Note you can also use ParmEd to convert to GROMACS after repartitioning.
This python script should do it:


import parmed as pmd

parm = pmd.load_file("prmtop", xyz="inpcrd"), 3.024).execute()"", format="GROMACS")"gromacs.gro", format="GRO")



Jason M. Swails
AMBER mailing list
Received on Tue Nov 09 2021 - 09:00:02 PST
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