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

Alan alanwilter at gmail.com
Thu May 16 12:37:07 CEST 2013

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

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.

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


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

More information about the gromacs.org_gmx-users mailing list