On Mon, Jan 13, 2025, Iglika Lessigiarska via AMBER wrote:
>
>
>I need to perform molecular dynamics simulations with Amber on protein-DNA
>complexes which contain Mg ions. The complexes have four protein chains
>and two DNA chains, while in the manual for MCPB.py in Amber 22 it is
>specified that "original_pdb This is the file name of the original PDB
>file, which should have only one chain.".
>
>Please kindly advice how/which tool I can use to prepare for molecular
>dynamics a protein-DNA complex containing more than one protein and DNA
>chains.
You should use a "nonbonded" metal ion model for Mg2+ with proteins and DNA.
You don't need MCPB.py for this.
Here are instructions:
https://ambermd.org/tutorials/advanced/tutorial20/12_6_4.php
I recommend "Example B", but others on the list are welcome to chime in.
Divalent ions in general are difficult to model, and there are number of
alternatives, many of which are cited in the above tutorial.
...good luck...dac
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Received on Mon Jan 13 2025 - 07:30:02 PST
