Hi Jason
Thank you for taking the time to answer me. I
I have installed ParmEd with all the updates to modify my prmtop file for simulations with HMR and it works great. So I will try it for the conversion from AMBER to GROMACS
Best
Stéphane
----------------------------------------------------------
Stéphane Abel, Ph.D., HDR
CEA Centre de Saclay
DRF/JOLIOT/I2BC-S/SB2SM/LBMS
Bat 528, Office 138C
Gif-sur-Yvette, F-91191 FRANCE
Phone (portable) : +33 6 49 37 70 60
________________________________________
De : Jason Swails [jason.swails.gmail.com]
Envoyé : mercredi 17 novembre 2021 04:16
À : AMBER Mailing List
Objet : Re: [AMBER] Can Parmed convert AMBER files to GROMACS made with the AMBER19SB ?
Hi Stephane,
I believe that ParmEd will convert Amber19SB to GROMACS just fine -- I
recommend just trying it. It's possible that the use of different CMAPs
between the same atom type names will cause issues in ParmEd when
translating to GROMACS (for non-CMAP terms, ParmEd always supports the
option of writing parameters directly to each valence term, but I don't
remember how the CMAP terms work).
You will have to write a script to do the conversion:
```
import parmed as pmd
parm = pmd.load_file("ff19SB.parm7", "ff19SB.rst7")
parm.save("ff19SB.top") # .top saves to GROMACS topology file format
parm.save("ff19SB.gro")
```
And execute it as `python <file.py>`. Does that work for you?
I recommend running an energy evaluation with both GROMACS and Amber to
ensure the energies match, however.
HTH,
Jason
On Mon, Nov 15, 2021 at 8:12 AM ABEL Stephane <Stephane.ABEL.cea.fr> wrote:
> Dear all,
>
> from a previous mail of Jason, I can use parmed for my task. But I have a
> question about the conversion feature of Pamed.
>
> It is possible to use it for converting AMBER parameter files into GROMACS
> ones if use the AMBER19SB force field since this force field contains an
> additional CMAP term in contrast to other AMBER force fields for protein?
>
> Thanks for your reply.
>
> Best
>
> Stephane
>
> ________________________________________
> De : ABEL Stephane
> Envoyé : mardi 9 novembre 2021 18:35
> À : AMBER Mailing List
> Objet : [PROVENANCE INTERNET] Re: [AMBER] Hydrogen Mass Repartitioning
> without ParmEd
>
> 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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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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>
--
Jason M. Swails
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Received on Wed Nov 17 2021 - 02:30:02 PST
