Dear Matias,
Thank you for taking the time to answer me.
>> ence, ff19SB should be portable to GROMACS, but new (ff19SB) atom types must be introduced. The other
>> thing is, porting also requires proper testing...
Indeed I found articles that use a conversion of AMBER19SB with GROMACS. But it is not clear to me how the conversion was done and well tested. That's why I asked this question.
>> While CHARMM CMAPs are corrections to the dihedral function, AMBER CMAPs represent the dihedral function..
This is indeed what I understand by reading the ff19SB paper of Carlos so the conversion in the GROMACS will not be easy to do. Thanks for the confirmation
Best
Stéphane
________________________________________
De : Matias Machado [mmachado.pasteur.edu.uy]
Envoyé : mardi 16 novembre 2021 16:06
À : AMBER Mailing List
Objet : Re: [AMBER] Can Parmed convert AMBER files to GROMACS made with the AMBER19SB ?
Dear Stephane,
You're right, GROMACS can support flexible CMAP definitions as headers in "cmap.itp" set the specific dihedral types. Hence, ff19SB should be portable to GROMACS, but new (ff19SB) atom types must be introduced. The other thing is, porting also requires proper testing...
I'm not the developer here, Carlos should better say, but despite using the same implementation, CHARMM and AMBER CMAPs mean slightly different things... While CHARMM CMAPs are corrections to the dihedral function, AMBER CMAPs represent the dihedral function...
I'm not a big fan of automagic porting... so I suggest you to start implementing ff19SB from a validated ffAMBER port of ff14SB (
https://www.gromacs.org/Downloads/User_contributions/Force_fields). Beware that GROMACS and AMBER use different energy units.
Last but not least, note that GROMACS code performs slower with CMAPs than without.
All the best,
Matías
----- Mensaje original -----
De: "Alan" <alanwilter.gmail.com>
Para: "AMBER Mailing List" <amber.ambermd.org>
Enviados: Martes, 16 de Noviembre 2021 5:28:13
Asunto: Re: [AMBER] Can Parmed convert AMBER files to GROMACS made with the AMBER19SB ?
Hi Stephane,
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.
>
This is not a stupid question but it should be addressed to GROMACS.
It's just a shame they stopped their mailing list. I stopped following
their new GROMACS Forum as I'm only interested in ACPYPE questions and I
don't have time to spare visiting their Forum, when filtered emails (like I
have here in Amber Mailing List) do this trick simple and quick.
If you get an answer there, please share it with us here.
Best
--
Alan Silva 🚲🏊♂🏃♂🇧🇷🇫🇷🇬🇧
PS: BTW, please Amber maintainers, please never stop this Mailing List.
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Received on Tue Nov 16 2021 - 10:00:02 PST
