On 13/08/2025 15:09, Stefan Ivanov via AMBER wrote:
> Dear Amber users,
> I need to generate Amber topologies for a set of platinum-containing compounds, the simplest of which is cisplatin ((NH3)2PtCl2, see below). I went over the MCPB.py tutorials and I see that I need to run antechamber and parmchk2 on the ligand structures without the metal ion before running MCPB.py. However, the ligands in those tutorials are entirely valid structures both with and without the metal ion. In contrast, if you remove the central, coordinating Pt ion from cisplatin, you are left with two completely disconnected and independent ammonia molecules and two Cl- ions. Does it even make sense two run antechamber and parmchk2 on such a structure?
>
> On the one hand, I can force antechamber to produce output on such a disconnected structure with the -dr flag set to 'no,' but does that even make sense? On the other hand, I know the metal ion should be a separate residue and is not supposed to be in the ligand structure given to antechamber. Right? Please advise how I should handle structures where the metal ion is central to a host of coordinated moieties.
> Sincerely,
> Stef
Hi Stefan,
I already told you and Hristo, you can't have a one-size-fits-all (or one-click-solves-all) solution for your platinum compounds. Also, you are going to have to customize your DFT calculations with
respect to the default scripts that MCPB produces, and the details depend on the specific compound.
Cheers,
Charo
--
Prof. Charo I. del Genio
Institute of Smart Agriculture for Safe and Functional Foods and Supplements, Trakia University, Stara Zagora, Bulgaria
Institute of Interdisciplinary Intelligent Science, Ningbo University of Technology, Ningbo, China
School of Mathematics, North University of China, Taiyuan, China
Editor in Chief of Chaos, Solitons & Fractals
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Received on Wed Aug 13 2025 - 05:30:03 PDT
