Hi Iglika,
Thanks for asking, and I totally agree with the suggestions provided previously.
Just one more thing: AMBER has a tutorial to help you build such a modified, non-bonded system.
https://ambermd.org/tutorials/advanced/tutorial20/m1264.php
It was written for TIP3P water, but please feel free to modify it for TIP4P-Ew. If so, some more parametrizations might be needed since the 12-6-4 model is water-dependent.
Best regards,
Zhen.
From: Solen Ekesan via AMBER <amber.ambermd.org>
Date: Monday, January 13, 2025 at 2:56 PM
To: iglika.biomed.bas.bg <iglika.biomed.bas.bg>, AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Amber metal ions protein multiple chains
[Apologies if this shows up twice...]
For divalent metal ions interacting with nucleic acids (DNA in your case), we recommend using TIP4P-Ew water model and the fine-tuned 12-6-4 divalent metal ion parameters (Example B as David Case mentioned). Check that you have the required lj_1264_pol.dat in your Amber directory ([Amber_dir]/dat/leap/parm/lj_12_6_4_pol.dat) - older versions might not have this.
If your Mg2+ ions are located at structurally/chemically important positions, I recommend restraining them while relaxing your solvent box. Nucleic acids simulations can be tricky, if you're new to nucleic acids I recommend also taking a look at the MTR1 ribozyme tutorial under "Case studies", specifically for neutralizing your system with Na+ ions, and the relaxation procedure.
Solen
Institute of Quantitative Biomedicine
Rutgers University
________________________________
From: David A Case via AMBER <amber.ambermd.org>
Sent: Monday, January 13, 2025 10:26 AM
To: iglika.biomed.bas.bg <iglika.biomed.bas.bg>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Amber metal ions protein multiple chains
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://urldefense.com/v3/__https://nam02.safelinks.protection.outlook.com/?url=https*3A*2F*2Fambermd.org*2Ftutorials*2Fadvanced*2Ftutorial20*2F12_6_4.php&data=05*7C02*7Cse310*40connect.rutgers.edu*7C4207c0cce8de468aede008dd33e6b1ad*7Cb92d2b234d35447093ff69aca6632ffe*7C1*7C0*7C638723788110809259*7CUnknown*7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ*3D*3D*7C0*7C*7C*7C&sdata=*2FPja9AypYh8*2Bymhl3aMlk*2B8zJWJ9kJU*2BTHXgdLx5Ro4*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJQ!!HXCxUKc!ylOAMcg9CqUdKzCoqYYjoKhU1xfEs77RjC8vDOmvYGsUhRo1v1H4vDh8I25Rrktvxe9i_foiNfyexrSIvZ_6fTQ$<
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https://urldefense.com/v3/__https://ambermd.org/tutorials/advanced/tutorial20/12_6_4.php__;!!HXCxUKc!ylOAMcg9CqUdKzCoqYYjoKhU1xfEs77RjC8vDOmvYGsUhRo1v1H4vDh8I25Rrktvxe9i_foiNfyexrSIgM7Eess$ >
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 - 12:30:03 PST
