[gmx-users] parametrization of protein-ligand covalent bond

[Leandro Bortot]

     Thanks Justin,

     The forcefield is AMBER99SB-ILDN, so that's following the standard
GAFF/Antechamber/acpype procedure with charge calculation at the HF/6-31G*
level.


Thank you for your attention,
Leandro.



On Mon, Mar 23, 2015 at 12:07 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/22/15 6:35 PM, Leandro Bortot wrote:
>
>> Dear users,
>>
>>       I need to simulate an inhibitor covalently bound to a protein. What
>> is
>> the best approach to get the parameters for adequately modeling the
>> protein-ligand bond and the new residue partial charges?
>>
>>       I was thinking about doing a standard parametrization using the
>> ligand
>> attached to the residue as my chemical entity. By doing this, I should
>> have
>> the parameters for the bond and the new partial charges.
>>
>>
> Sounds reasonable.  What does the parametrization for the parent force
> field call for?
>
> -Justin
>
> --
> ==================================================
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
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> University of Maryland, Baltimore
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> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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