[gmx-users] updates about ACPYPE

[Alan]

Hi,

Please use svn checkout
http://ccpn.svn.sourceforge.net/svnroot/ccpn/branches/stable/ccpn/python/acpype
 acpype

Google Code will be retired and is not writable anymore.

The latest version is:

ACPYPE: AnteChamber PYthon Parser interfacE v. 2015-11-02 10:03:43Z Rev:
8810 (c) 2015 AWSdS

I am trying to look at the Urey-Bradley potential but I can’t promise
anything.

It should still be compatible with GMX 4 and 5, but now parameters are
generated to GMX 4.5/5 by default. I am not aware of any issue.

Thanks,

Alan


On 22 October 2015 at 02:27, yunshi11 . <yunshi09 at gmail.com> wrote:

> Hi Alan,
>
> Is this Rev: 403? And does the --gmx45 still compatible with gromacs5
> (although gromacs says its version 5 is mostly backward compatible with
> version 4)?
>
> On Sat, Aug 30, 2014 at 8:40 PM, Alan <alanwilter at gmail.com> wrote:
>
> > 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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> >
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-- 
Alan Wilter SOUSA da SILVA, DSc
Senior 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