Re: [AMBER] Hydrogen Mass Repartitioning without ParmEd

From: ABEL Stephane <>
Date: Tue, 9 Nov 2021 15:40:33 +0000

Hi Saleh,

>> I use Charmm-Gui to generate the input files for hydrogen masserepartitioning simulation using Amber

Your suggestion useful and indeed it is possible to use CHARMM-GUI for this task . But since my objective is to do simulations with GROMACS I have to convert the AMBER inpcrd/prmtop files into GROMACS files using acepype. And unfortunately acepype does not support parm7 file (generated by CHARMM-GUI)



Stéphane Abel, Ph.D., HDR
CEA Centre de Saclay
Bat 528, Office 138C
Gif-sur-Yvette, F-91191 FRANCE
Phone (portable) : +33 6 49 37 70 60
De : Alyemni, Saleh []
Envoyé : mardi 9 novembre 2021 16:06
À : AMBER Mailing List
Objet : Re: [AMBER] Hydrogen Mass Repartitioning without ParmEd

Hi Stephane,

I use Charmm-Gui to generate the input files for hydrogen mass repartitioning simulation using Amber, and it works fine for me, give it a try. I prepare my whole system inside Charmm—Gui then at the final step I choose generate input files for Amber and click on Hydrogen mass repartitioning (HMR) so it generate HMR input files for Amber. Hope this will work for you.


Saleh AlYemni
PhD Candidate, UCL School of Pharmacy
From: Jason Swails <>
Sent: Tuesday, November 9, 2021 2:35:36 PM
To: AMBER Mailing List <>
Subject: Re: [AMBER] Hydrogen Mass Repartitioning without ParmEd

⚠ Caution: External sender

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.


On Tue, Nov 9, 2021 at 8:50 AM ABEL Stephane <> 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
> _______________________________________________
> AMBER mailing list

Jason M. Swails
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Received on Tue Nov 09 2021 - 08:00:02 PST
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