[AMBER] How to build one metal ions surrounding with two ligands by MCPB.py

From: ning <realdancer_wn.126.com>
Date: Sat, 25 Dec 2021 11:35:38 +0800 (CST)

Dear Amber experts,

      Recently, I need to build a regular MD system that contains one metal ion (MG), two ligands (ADP and PO4) and protein. For the metal bonded model building, MCPB.py software was used to construct the model, however, the Metal ion MG was surrounded by ADP and PO4, and the distances between metal MG and ligands were both near to 3 angstrom. I'm not sure whether MCPB.py could build metal ions with two ligands. And I added another ligand parameter into the tail of the input file forcibly, whereas, MCPB.py reported a failure. Here is my modified input file:

original_pdb complex-h.pdb
group_name com
cut_off 2.8
ion_ids 5855
ion_mol2files MG.mol2
naa_mol2files ADP.mol2
frcmod_files ADP.frcmod
naa_mol2files PO4.mol2
frcmod_files PO4.frcmod
large_opt 1

Please help me, any suggestions are welcome. Thanks in advance.

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Received on Fri Dec 24 2021 - 20:00:02 PST
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