[gmx-users] binding free energy

[Billy Williams-Noonan]

Just to clarify, the formula should be:

   dG (bind)  = dG (complex) - dG (solv)

Billy

On Tuesday, 5 July 2016, Billy Williams-Noonan <
billy.williams-noonan at monash.edu> wrote:

> You would want to perturb your amino acid in both the free (unbound) and
> complex (bound) aqueous states.
>
> Then if you subtract the free energy change from perturbing the free
> ligand, from that of perturbing the bound ligand, you should close the
> non-physical thermodynamic cycle and get a binding free energy.
>
> But you will need to make sure everything in your simulation is
> parameterised properly to get an accurate value.  You will also need to
> make sure you have sufficient sampling time and lambda states.
>
> Good luck!
>
> Billy
>
> On Tuesday, 5 July 2016, Alexander Alexander <alexanderwien2k at gmail.com>
> wrote:
>
>> Dear gromacs user,
>>
>> I was wondering if anybody has any experience with binding free energy
>> calculation of a molecule (here amino acid) into a solid surface in
>> aqueous
>> solution using alchemical analysis?
>>
>> I have already tried successfully the tutorial of methane solvation free
>> energy in water and some other examples, but looks all of them are
>> solvation free energy and not binding free energy!
>>
>> Thanks.
>> Regards,
>> Alex
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
>
> --
> Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon
>
> *LinkedIn Profile
> <http://www.linkedin.com/profile/preview?locale=en_US&trk=prof-0-sb-preview-primary-button>
> **|*   +61420 382 557
>
> Monash Institute for Pharmaceutical Sciences ( *MIPS* )
> Royal Parade, Parkville, 3052
>
>
>

-- 
Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon

*LinkedIn Profile
<http://www.linkedin.com/profile/preview?locale=en_US&trk=prof-0-sb-preview-primary-button>
**|*   +61420 382 557

Monash Institute for Pharmaceutical Sciences ( *MIPS* )
Royal Parade, Parkville, 3052