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

[Alan]

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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Alan Wilter SOUSA da SILVA, DSc
Senior Bioinformatician, UniProt
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