Hi,
Thanks for your reply.
The ligand interaction from
https://www.rcsb.org/3d-view/4QM9?preset=ligandInteraction&sele=CYS
has indicated that CYS is actually a CYM, as what you said.
And I dealt with this CYS as an organic molecule, not a CYM residue.
The antechamber and parmchk2 did a good job on typing this ligand.
Best,
Yuan
> -----原始邮件-----
> 发件人: "Matias Machado" <mmachado.pasteur.edu.uy>
> 发送时间: 2018-08-16 05:59:18 (星期四)
> 收件人: "AMBER Mailing List" <amber.ambermd.org>
> 抄送:
> 主题: Re: [AMBER] HOW to type a free CYS molecule
>
> Dear Yuan,
>
> I don't know what you want to do... buy the CYS you are referring in structure 4QM9 is composing a metallic center with 3 HIS to coordinate a Fe atom... so it's not just a "free reduced CYS" but most probably a CYM (deprotonated CYS or thiolate anion)
>
> You may get some hints from this tutorial [http://ambermd.org/tutorials/advanced/tutorial1_orig/]
>
> Best,
>
> Matías
>
> ------------------------------------
> PhD.
> Researcher at Biomolecular Simulations Lab.
> Institut Pasteur de Montevideo | Uruguay
> [http://pasteur.uy/en/laboratorios-eng/lsbm]
> [http://www.sirahff.com]
>
> ----- Mensaje original -----
> De: "MinYuan" <minyuan.mail.ustc.edu.cn>
> Para: amber.ambermd.org
> Enviados: Miércoles, 15 de Agosto 2018 10:57:13
> Asunto: [AMBER] HOW to type a free CYS molecule
>
> Hi,
>
>
> I'm studying a free CYS molecule, HS-CH2-CH(HN3+)-COO-.
> This free CYS is a ligand in the protein (PDB ID 4QM9).
>
>
> I tried to use antechamber and parmchk2 to type this CYS, HS-CH2-CH(HN3+)-COO-.
> But failed.
>
>
> Does any one known how to type a free CYS molecule?
>
>
> Thanks.
>
>
> Best,
>
>
> Yuan
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Received on Wed Aug 15 2018 - 20:00:02 PDT
