[gmx-users] i have queston about partial charge zinc

[Alan]

The original online server at the University of Cambridge has been retired
after almost 8 years of service I'm sorry. The machine there was really
outdated and impossible to update ACPYPE with new features we've developed
in the past couple of years.

We are working to have the new one up and running but unfortunately I can
predict a date for the return.

For sure, we will announce in the proper channels when the new server is up.

Sorry for the inconvenience,

Alan

On Sun, 30 Sep 2018 at 09:11, neelam wafa <neelam.wafa at gmail.com> wrote:

> Hi !
> Alan the link for updated acpype you have shared is all about the
> downloadable tool. Can you please share the link for online server for
> it. and is their any tutorial to explain the changed protocol.
> looking forward for your cooperation.
>
> Regards
>
> On 9/20/18, Alan <alanwilter at gmail.com> wrote:
> > Please, official, original, updated ACPYPE is now here:
> > https://github.com/alanwilter/acpype
> >
> > Alan
> >
> > On 20 September 2018 at 13:56, Andrea Coletta <andrea.coletta at chem.au.dk
> >
> > wrote:
> >
> >> In general I would say that +2 is not a good choice, since it seems to
> me
> >> that this is a Zinc complex.
> >>
> >> You may want to look at this:
> >>
> >> http://ambermd.org/tutorials/advanced/tutorial20/ZAFF.htm
> >>
> >> you should be able to create the topology in ambertools and then convert
> >> it to gromac with acpype (https://github.com/llazzaro/acpype)
> >>
> >> -----Original Message-----
> >> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:
> >> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of milad
> >> bagheri
> >> Sent: 20. september 2018 14:28
> >> To: gromacs.org_gmx-users at maillist.sys.kth.se
> >> Subject: [gmx-users] i have queston about partial charge zinc
> >>
> >> Hi
> >> I gonna MD simulation a protein that contained a zinc ion for build
> >> topology I used from the amber99sb  force field Atomic charge is written
> >> "+2" in topology.
> >> I wanted to ask if this charge is correct or should be calculated in a
> >> different way?
> >> "PDB id 4row"
> >> sincerely
> >> --
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> >>
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> >
> >
> >
> > --
> > I'll cycle across Britain in 2018 for a charity, would you consider
> > supporting my cause? http://uk.virginmoneygiving.com/AlanSilva
> > Many thanks!
> > --
> > 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
> > --
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-- 
*I**​ have just cycled* from Land's End to John O'Groats​​​ (the
whole Britain!)
for a charity, would you consider​ ​supporting my​ cause?
http://uk.virginmoneygiving.com/AlanSilva
--
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