Speaking more as a programmer:
> *step-wise* how to perform the total calculation.
1. Make pdb of solvent molecule
2. Follow a tutorial for creating an amber model of that molecule from
the pdb
2a. Basic step: assign atom types
2b. Basic step: derive charges
3. Create a box of your solvent, e.g. by solvating one molecule with itself
4. Equilibrate the box, run dynamics [maybe you are at the 1 month mark]
5. Verify bulk properties of the solvent with experiment; iterate tuning
atom type parameters and/or charges
6. For each molecule you want to solvate
Follow 1-2 for that molecule
Solvate it in a box derived from your final equilibrated solvent box
Equilibrate
Perturb/Disappear the molecule? Numerous times?
I haven't done the latest methods for the last step, so you will need to
research it some more, but this gives an idea of the scope of the setup.
The level of parameterization can range from cheap to a project in its
own right.
Bill
On 9/3/17 9:57 PM, Debasish Mandal wrote:
> Dear AMBER Users,
> I am a novice in molecular
> dynamics. I would like to calculate the binding (free) energy of a series
> of molecules in a particular ionic liquid. I have planned to parameterize
> both the solvent and solute molecule and then put a single solute molecule
> in the solvent molecule box. Then further processes (*which I actually have
> no clear idea*) for calculating binding (free) energy can be done. I will
> be highly thankful if you help me by providing responses of my following
> queries.
>
>
>
> 1. Is this calculation is possible in AMBER?
>
> 2. Is this approach is correct
>
> ?
>
> 3. If somebody has better idea to perform this calculation please let
> me know.
>
> 4. Please provide me some details
> in
> *step-wise* how to perform the total calculation.
>
>
>
> Your help will be highly appreciated.
>
>
>
> Thanks & Regards
>
>
>
> Debasish
>
>
>
> ======================================
> Debasish Mandal
> Post Doctoral Research Fellow
> C/o- Prof. Sason Shaik
> Institute of Chemistry
> The Hebrew University of Jerusalem,
> Givat Ram Campus,
> Jerusalem, 91904, Israel
> E-mail: debu1500.gmail.com
> Mob.No-08017296958
>
>
>
> “I’m thankful to all those who said ‘NO’ to me it's because of them, I did it
>
> myself” Einstein
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sun Sep 03 2017 - 22:30:02 PDT
