Dear all
Regarding modelling of Mg-DNA-protein systems, applying the fine-tuned
12-6-4 divalent metal ion parameters with parmed add12_6_4 command I get
the following error message:
"LJ12_6_4Error: Polarizability parameter of AMBER_ATOM_TYPE H is not the
same as that of AMBER_ATOM_TYPE HO, but their VDW parameters are the
same."
I understand that the method requires atom types with the same VDW
parameters to have the same polarizability parameters, but I prepared the
system by deleting all H atoms with pdb4amber and adding them in tleap.
The atom types H and HO are added to the system by tleap, and they have
different polarizabilities than HO in lj_12_6_4_pol.dat.
Please advice how I can overcome this error.
Thank you
Iglika
> 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!
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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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>> >
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Received on Tue Feb 04 2025 - 04:30:02 PST
