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.
Best wishes,
Fabian
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
http://bku.technion.ac.il
> On 17 Nov 2015, at 4:17 PM, Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk> wrote:
>
> Hi,
>
> Have a look into tutorial A9 and see if that can work for you.
> Alchemical transformations can be done both "absolute" (the definition
> of "small molecule" may be a question here) and relative (usually such
> that changes are small). In this context, you may want to look into the
> work done by David Mobley, in particular FreeSolv (a database of
> absolute free energies of quite a large number of "small"
> organic molecules).
>
> Cheers,
> Hannes.
>
>
> On Tue, 17 Nov 2015 15:51:50 +0200
> Fabian gmail <fabian.glaser.gmail.com> wrote:
>
>> Hi,
>>
>> Is there a way in Amber to compute the free energy of solvation of a
>> single small molecule, using a mixture of solvents?
>>
>> I know how to prepare the solvent mixture with packmol and the small
>> molecule and peform the simulation, my question is about the
>> calculation itself. I am interested to compare several different
>> drugs in several different solvent mixtures.
>>
>> If somebody has done something similar and can give me some inputs or
>> direct me some relevant papers I will much appreciate that.
>>
>> Thanks a lot,
>>
>> Fabian
>>
>>
>>
>>
>> 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
>> http://bku.technion.ac.il
>>
>>
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>
>
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Received on Tue Nov 17 2015 - 08:00:04 PST
