Great to know, thank you very much !
BTW, the AU ions can be found quite often in the cofactor site of some
enzymes involved in redox ..
All the best
Enrico
Il giorno ven 22 nov 2024 alle ore 14:38 Li, Zhen <lizhen6.chemistry.msu.edu>
ha scritto:
> Hi Enrico,
>
> I can offer two cents on that question. First, Au(I) is not as common as
> gold metal substance. Second, there is no experimental hydration free
> energy (HFE) and ion-oxygen distance (IOD) data to serve as parametrization
> targets for Au(I) (feel free to correct if my information is out of date).
>
> If you could kindly provide any experimental or ab initio data for Au(I)’s
> HFE and IOD, as well as the water model you are interested for your
> simulation, I can do a quick parametrization and get back to you in about a
> week.
>
> External resource: https://pubs.acs.org/doi/abs/10.1021/acs.jcim.0c01390
>
> Best regards,
> Zhen
>
> Enrico Martinez via AMBER：
>
> So what are the reasons of the absence for the parameters for AU+1
> assuming
> that we have other +1 metals ?
> Enrico
>
>
> Il giorno gio 21 nov 2024 alle ore 20:33 ışılay öztürk <
> isilayozturk.gmail.com> ha scritto:
>
>
> Hi Enrico,
>
>
> For the parametrized gold region, you can take a look
>
>
> https://urldefense.com/v3/__https://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.php__;!!HXCxUKc!xBDZd1PzpCn8pxfiqp6SozgE57TduB4A9JsNBmUZXZO3-7yH7LFz92sXn5tLzfpWWffxKyyK1B20K_k6a00OyTg$
>
> and this paper
> https://urldefense.com/v3/__https://doi.org/10.3390/molecules29184416__;!!HXCxUKc!xBDZd1PzpCn8pxfiqp6SozgE57TduB4A9JsNBmUZXZO3-7yH7LFz92sXn5tLzfpWWffxKyyK1B20K_k6vjVc5MU$
>
>
> Good luck!
>
>
> Best
>
> Işılay
>
>
>
> Enrico Martinez via AMBER <amber.ambermd.org>, 21 Kas 2024 Per, 14:00
>
> tarihinde şunu yazdı:
>
>
> Dear Amber users!
>
>
> I am trying to parametrize the protein containing 3 gold ions defined as
>
> AU
>
> in the pdb structure, using the following parameters.
>
>
> source leaprc.protein.ff14SB
>
> source leaprc.water.tip3p
>
> #source leaprc.DNA.OL15
>
> #source leaprc.RNA.OL3
>
> #source leaprc.gaff2 # optimonally for ligand
>
>
>
> This is the error which I get from tleap.
>
>
> FATAL: Atom .R<AU 589>.A<AU 1> does not have a type.
>
> FATAL: Atom .R<AU 590>.A<AU 1> does not have a type.
>
> FATAL: Atom .R<AU 591>.A<AU 1> does not have a type.
>
>
> How the gold be parametrized ??
>
>
> Many thanks in advance !
>
>
> Enrico
>
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Received on Fri Nov 22 2024 - 09:00:02 PST
