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://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$<https://urldefense.com/v3/__https:/nam02.safelinks.protection.outlook.com/?url=https*3A*2F*2Fambermd.org*2Ftutorials*2Fadvanced*2Ftutorial20*2F12_6_4.php&data=05*7C02*7Cse310*40connect.rutgers.edu*7C4207c0cce8de468aede008dd33e6b1ad*7Cb92d2b234d35447093ff69aca6632ffe*7C1*7C0*7C638723788110809259*7CUnknown*7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIl!
YiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ*3D*3D*7C0*7C*7C*7C&sdata=*2FPja9AypYh8*2Bymhl3aMlk*2B8zJWJ9kJU*2BTHXgdLx5Ro4*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJQ!!HXCxUKc!ylOAMcg9CqUdKzCoqYYjoKhU1xfEs77RjC8vDOmvYGsUhRo1v1H4vDh8I25Rrktvxe9i_foiNfyexrSIvZ_6fTQ$>
> <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 Tue Jan 21 2025 - 02:30:02 PST
