Hi Iglika,
Everything mentioned, TIP4-EW water and 12-6-4 parameters for divalent metal ions etc., are compatible with proteins.
The the fine-tuned parameters (i.e. Panteva corrections) mentioned earlier only make pair-wise adjustments between Mg2+ and the nucleic acid atoms and therefore no other component of the system is affected.
You would simply source your protein force field along with the DNA, water and divalent metal ions force fields/parameters and your system should build fine (assuming no unrelated issues). I would still recommend equilibrating your solvent following the nucleic acid tutorials. Once a nucleic acid molecule loses structural properties it almost never can recover it, and these depend highly on the solvent environment around it.
Good luck!
Solen
________________________________
From: iglika.biomed.bas.bg <iglika.biomed.bas.bg>
Sent: Tuesday, January 21, 2025 4:52 AM
To: Li, Zhen <lizhen6.chemistry.msu.edu>; AMBER Mailing List <amber.ambermd.org>
Cc: Solen Ekesan <solen.ekesan.rutgers.edu>; iglika.biomed.bas.bg <iglika.biomed.bas.bg>
Subject: Re: [AMBER] Amber metal ions protein multiple chains
Dear David, Solen, and Zhen
Thank you for providing me with the information for modelling of Mg-DNA
systems. I also have protein chains in the complex (it is protein-DNA-Mg
complex). Please let me know whether the method you recommended is also
suitable for such complexes, as I saw that in the examples only DNA and Mg
are present in the starting pdb files.
Thank you in advance
Best regards
Iglika
> 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://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fambermd.org%2Ftutorials%2Fadvanced%2Ftutorial20%2Fm1264.php&data=05%7C02%7Cse310%40connect.rutgers.edu%7C0810252cdd374ad6632508dd3a01d52d%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C638730501788847131%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=59DfJPJriAxRES5fhOJxH3MwfLipg3YwRKktLiT009o%3D&reserved=0<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://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fnam02.safelinks.protection.outlook.com%2F%3Furl%3Dhttps*3A*2F*2Fambermd.org*2Ftutorials*2Fadvanced*2Ftutorial20*2F12_6_4.php%26data%3D05*7C02*7Cse310*40connect.rutgers.edu*7C4207c0cce8de468aede008dd33e6b1ad*7Cb92d2b234d35447093ff69aca6632ffe*7C1*7C0*7C638723788110809259*7CUnknown*7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ*3D*3D*7C0*7C*7C*7C%26sdata%3D*2FPja9AypYh8*2Bymhl3aMlk*2B8zJWJ9kJU*2BTHXgdLx5Ro4*3D%26reserved%3D0__%3BJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJQ!!HXCxUKc!ylOAMcg9CqUdKzCoqYYjoKhU1xfEs77RjC8vDOmvYGsUhRo1v1H4vDh8I25Rrktvxe9i_foiNfyexrSIvZ_6fTQ%24&data=05%7C02%7Cse310%40connect.rutgers.edu%7C0810252cdd374ad6632508dd3a01d52d%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C638730501788863442%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=LGTEOaGfLPedDq3jdpY4QVfVdaR9BGpjAKXGDqgZM0E%3D&reserved=0<https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fnam02.safelinks.protection.outlook.com%2F%3Furl%3Dhttps*3A*2F*2Fambermd.org*2Ftutorials*2Fadvanced*2Ftutorial20*2F12_6_4.php%26data%3D05*7C02*7Cse310*40connect.rutgers.edu*7C4207c0cce8de468aede008dd33e6b1ad*7Cb92d2b234d35447093ff69aca6632ffe*7C1*7C0*7C638723788110809259*7CUnknown*7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIl&data=05%7C02%7Cse310%40connect.rutgers.edu%7C0810252cdd374ad6632508dd3a01d52d%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C638730501788875334%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=4R%2F9b6OHNpV5H5UNGhbltq9U7GrIhxQ%2B0YjKS7vkhhc%3D&reserved=0!<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://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fambermd.org%2Ftutorials%2Fadvanced%2Ftutorial20%2F12_6_4.php__%3B!!HXCxUKc!ylOAMcg9CqUdKzCoqYYjoKhU1xfEs77RjC8vDOmvYGsUhRo1v1H4vDh8I25Rrktvxe9i_foiNfyexrSIgM7Eess%24&data=05%7C02%7Cse310%40connect.rutgers.edu%7C0810252cdd374ad6632508dd3a01d52d%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C638730501788886585%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=3QUrT2M%2BJFZ%2BWXnllCicrVKMQt4PaD2ZQHk9%2FpZMCwM%3D&reserved=0
> >
>
> 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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