Thanks again for your help Jason. I will try with miniconda
As I have also seen that you posted a message in the ParmEd forum aboit the use of parm7 and rst7 (generated with CHARMM-GUI) files with acepype
*
https://githubmemory.com/repo/ParmEd/ParmEd/issues/1117
Q: It is possible to use acepype with a parm7 and rst7 files generated by CHARMM-GUI with HMR
A: These are the same file types. parm7 is a synonym for prmtop and rst7 is a synonym for inpcrd. You can use ACPYPE as-is."
AFAIK ut is not documented in the acepype website
So Thank you a lot Jason (and Saleh) with your help I think I have resolved my problem.
Best
Stéphane
________________________________________
De : Jason Swails [jason.swails.gmail.com]
Envoyé : mardi 9 novembre 2021 17:46
À : AMBER Mailing List
Objet : Re: [AMBER] Hydrogen Mass Repartitioning without ParmEd
On Tue, Nov 9, 2021 at 10:21 AM ABEL Stephane <Stephane.ABEL.cea.fr> 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")
pmd.tools.HMassRepartition(parm, 3.024).execute()
parm.save("gromacs.top", format="GROMACS")
parm.save("gromacs.gro", format="GRO")
-------------------
HTH,
Jason
--
Jason M. Swails
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Received on Tue Nov 09 2021 - 10:00:02 PST
