Re: [AMBER] free energy of solvation of small molecules

From: Fabian gmail <>
Date: Thu, 19 Nov 2015 18:40:19 +0200

Dear Hannes,

Sorry to bother you, I went through the A9 tutorial in detail, and I have several additional questions to my specific goals and molecules:

I am not sure how to construct my thermodynamic cycle, in my case there is no protein, only two different ligands, for what I saw in your tutorial cycle, you need a protein medium to run MD and mutate the ligand. In my case the protein medium does not exist and the ligands are very big and quite different… I would prefer not to mutate them if possible.

Another possibility for me would be to run two different type of solvents, one would be the ligand in pure water and the other in water + acetone for example and calculate the difference between the two ligands. And then I would calculate the DG of transfer between water to water + acetone or the hydration in water + acetone, which is very close to what really happens, Is this doable with TI?

Additionally, the ligands I consider are very very flexible large and different see them: <> <>

Can they be mutated into each other without accumulating charge errors?

I think I would prefer not to mutate them but to calculate the hydration free energies of each of them in water and / or in water + acetone mixtures.

Is that a good approach?

Thansk a lot again,


Dr. Fabian Glaser
Head of the Structural Bioinformatics section

Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa 32000, ISRAEL

fglaser at technion dot ac dot il
Tel: +972 4 8293701

> On 17 Nov 2015, at 6:06 PM, Hannes Loeffler <> wrote:
> On Tue, 17 Nov 2015 17:35:04 +0200
> Fabian gmail <> wrote:
>> Dear Hannes,
>> Thanks a lot, it looks very interesting and relevant, my molecules
>> are much larger (ritonavir and darunavir) but still I maybe able to
>> use similar ideas.
> Regarding the number of atoms the following may be of use
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Received on Thu Nov 19 2015 - 09:00:05 PST
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