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

[neelam wafa]

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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>
>
>
> --
> 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
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