Hi Franz,
thanks that's very helpful. Amber uses the residue name inside Leap while
it is building the topology, but inside the final topology file itself the
cmaps are specified using atom number and cmap id (pointing to a table of
cmaps that are stored in the topology file itself), so no residue name is
needed. I'm not sure why Jason suggested that the prmtop uses the residue
name (unless I misunderstood his comment on the github issue). It sounds
like converting what is in the Amber prmtop to something needed for gromacs
should be straightforward. As I said I'm not familiar myself with how
gromacs implements cmaps or how they are stored. Does it assign cmaps based
on atom type?
carlos
On Wed, Jun 21, 2023 at 10:29 AM Franz Waibl via AMBER <amber.ambermd.org>
wrote:
> Dear Carlos, dear Amber users,
>
> thanks for the reply. I am aware that Amber is free for academic use
> (thanks for that, by the way!), but it would still be useful to be able
> to run ff19SB simulations on Gromacs, e.g., to use algorithms that are
> not implemented in Amber.
>
> Gromacs does support multiple CMAPs. If I understand correctly, the
> problem is that ff19SB CMAP terms depend on the residue name in addition
> to the atom type. To convert the topology correctly, one would have to
> define separate atom types for the CA atom of each amino acid (XC1, XC2,
> ...). This also seems to be what CHARMM-GUI is doing (see the Github
> issue mentioned before).
> In fact, I ran a very short test simulation in Amber and compared the
> results to energy values from gmx mdrun -rerun. After manually tweaking
> the topology as described above, I was able to obtain consistent CMAP
> energies between Amber and Gromacs.
>
> However, it is very tedious to do this manually for a larger system, so
> a ParmEd-based solution would be highly appreciated.
>
> Best regards,
> Franz
>
>
> On 21.06.23 15:14, Carlos Simmerling wrote:
> > My understanding is that the issue is on the gromacs end, not parmed.
> > I'm not a gromacs user but you could ask them if multiple cmaps are
> > supported. If yes, then we can work to update the conversion process.
> > Alternatively, Amber is free and has a good library of tutorials.
> > Carlos
> >
> > On Wed, Jun 21, 2023, 8:59 AM Franz Waibl via AMBER
> > <amber.ambermd.org> wrote:
> >
> > Dear Amber users,
> >
> > I would like to run simulations with the Amber-ff19SB forcefield on
> > Gromacs. I have seen an Issue on Github
> > (https://github.com/ParmEd/ParmEd/issues/1292) stating that ParmEd
> > does
> > not handle the CMAP term conversion correctly. I also ran some tests
> > with the ParmEd version in Ambertools23 installed via conda, and it
> > seems that the same problem occurs: Only one set of CMAP
> > parameters is
> > written to the Gromacs topology, rather than different parameters for
> > each amino acid.
> >
> > Do you know if this problem can be avoided somehow in ParmEd? If no,
> > what is the recommended way to obtain ff19SB topologies for Gromacs?
> >
> > Thanks for your help.
> >
> > Best regards,
> > Franz
> >
> > --
> > ETH Zürich
> > Franz Waibl
> > Lab. für Physikalische Chemie
> > HCI G 227
> > Vladimir-Prelog-Weg 1-5/10
> > 8093 Zürich
> >
> > Telefon +41 44 632 55 04
> > franz.waibl.phys.chem.ethz.ch
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> --
> ETH Zürich
> Franz Waibl
> Lab. für Physikalische Chemie
> HCI G 227
> Vladimir-Prelog-Weg 1-5/10
> 8093 Zürich
>
> Telefon +41 44 632 55 04
> franz.waibl.phys.chem.ethz.ch
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Jun 21 2023 - 08:00:02 PDT
