Hi Carlos,
Thank you for taking the time to answer me. But, sorry I don't understand your answer or I missed an important thing , here.
GROMACS has been supporting CMÄP for different Amino acids for a long time and I often use it with CHARMM36 force field. Is the CMAP approach of AMBER19SB different from CHARMM36 one ? Sorry if it is a stupid question.
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 : Carlos Simmerling [carlos.simmerling.gmail.com]
Envoyé : lundi 15 novembre 2021 14:28
À : AMBER Mailing List
Objet : Re: [AMBER] Can Parmed convert AMBER files to GROMACS made with the AMBER19SB ?
to my knowledge, GROMACS does not have code support for using different
CMAPs for different amino acids, so even if you could convert the file it
would not work properly. Perhaps you can contact GROMACS developers and see
if the code has been updated.
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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Received on Mon Nov 15 2021 - 08:00:02 PST
