[gmx-users] About AMBER Force field SB 2012 (ff12SB), using ACPYPE

Mark Abraham mark.j.abraham at gmail.com
Thu May 16 18:19:44 CEST 2013

On Thu, May 16, 2013 at 12:37 PM, Alan <alanwilter at gmail.com> wrote:

> With ACPYPE I can convert any Amber *.prmtop and *.crd to Gromacs, but it
> doesn't mean it will work straightforward (but I am working for that).
> For example, I am wondering how Gromacs team will port the Amber FF12SB,

There's no plan to do so, but if someone wants to do so and can demonstrate
they've done it correctly (e.g. suitable agreement with the native version)
then contributions are always welcome.

> since now we have atom types like '2C', '3C' (ie. starting with a number),
> and GMX top won't accept this.

What is the specific issue?

Of course, a simple solution is to do '2C' -> 'a2C' for example (and that
> works with grompp 4.6.1), but I am wondering what GMX developers would do
> here first, since using 3-letters wouldn't be a nice style.

Offhand, I can't think of a good reason to require an atom type to start
with a letter, but there are a lot of hidden gotchas about how GROMACS
parse lots of ugly file formats under lots of conditions...

I am about to implement this workaround for ACPYPE, but just checking first
> if someone has a better idea/suggestion.

Seems OK to me, offhand, but I don't have anything like full information,
or time to get it :-(


> Alan
> --
> Alan Wilter SOUSA da SILVA, DSc
> Bioinformatician, UniProt - PANDA, EMBL-EBI
> CB10 1SD, Hinxton, Cambridge, UK
> +44 1223 49 4588
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