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
Thanks
Stéphane
________________________________________
De : Jason Swails [jason.swails.gmail.com]
Envoyé : mardi 9 novembre 2021 15:35
À : AMBER Mailing List
Objet : Re: [AMBER] Hydrogen Mass Repartitioning without ParmEd
tleap does not currently support writing a topology file with repartitioned
masses, and ParmEd is the only option for repartitioning within Amber.
If you describe what you mean by "some reasons", maybe it's straightforward
to make ParmEd work for you.
HTH,
Jason
On Tue, Nov 9, 2021 at 8:50 AM ABEL Stephane <Stephane.ABEL.cea.fr> wrote:
> Dear all
>
> I have a silly question. For some reasons I can not use ParmEd but would
> like to perform MD with Hydrogen Mass Repartitioning approach. So it is
> possible to modify a prmtop file and adjust the C and H masses without
> using ParmEd but using for instance tleap or another Amber tools ?
>
> Thank you
>
> Stephane
>
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>
--
Jason M. Swails
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Received on Tue Nov 09 2021 - 07:30:02 PST
