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

[Mark Abraham]

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 :-(

Mark


>
> 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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