[gmx-users] updates about ACPYPE
alanwilter at gmail.com
Sat Aug 30 12:41:29 CEST 2014
Many thinks for all of you who uses ACPYPE and my sincere apologises for
those who have been facing issues when running ACPYPE in “amb2gmx” module
to convert to Gromacs files with Amber Forcefields 12SB and 14SB.
I am aware of this issue for more than a year, since AmberTools13 were
The problem is simple: Amber new forcefields introduced new atom types
whose names start with a digit, and Gromacs does not accept them. The
simply solution is to prefix these atom types with any letter.
I am really sorry for not doing it straightforward a year ago. Mostly lack
of time to consider some further implications, mainly how/if Gromacs would
handle these new FF12SB and FF14SB, which is still an open question.
So, for downloading or updating ACPYPE, please have a look at:
or simply (for those who already have ACPYPE):
Alan Wilter SOUSA da SILVA, DSc
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Cambridge CB10 1SD
Tel: +44 (0)1223 494588
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