Dear community,
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
released.
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:
https://code.google.com/p/acpype/
Install anew:
svn checkout
http://ccpn.svn.sourceforge.net/svnroot/ccpn/branches/stable/ccpn/python/acpype
acpype
or simply (for those who already have ACPYPE):
svn update
Many thanks,
Alan
--
Alan Wilter SOUSA da SILVA, DSc
Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588
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Received on Sat Aug 30 2014 - 04:00:02 PDT
