Thanks dear Vlad for your complete answer, I agree with you.
But the only problem is that, when I attempt to run an independent simulation for my ligand into the explicit solvation, ligand exposes very different conformations during MD simulation and this lead to the different internal energies so the delta free energy value is effected from this event. How can I solve this point?
Thanks,RS
On Saturday, May 9, 2015 1:23 PM, Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de> wrote:
Dear Ramin,
If you go for the absolute dG, probably best is to have 3 trajectories
(possibly multiple trajectories for each system would be even better).
Even so, accurate dGs are very challenging with MMPBSA. However, for ddG
(relative), one trajectory of the complex may be enough (possibly
multiple independent trajectories of the complex would be better).
Best wishes
Vlad
On 09.05.2015 12:09, Ramin Ekhteiari wrote:
> I upgraded my email, I hope my messages are not placed in Spam box.
>
> Berk.
>
>
>
> On Saturday, May 9, 2015 5:17 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
>
> you need to 'upgrade' your email. For some reasons, email from yahool is
> automatically moved to spam folder in gmail
>
> Hai
>
> On Mon, May 4, 2015 at 2:06 PM, Ramin Ekhteiari <ramin_ekh.yahoo.com> wrote:
>
>> Hi Dear Amber users,
>> I would like to calculate delta free energy value between a ligand and its
>> receptor, for this purpose I performed only one MD simulation for my
>> complex (ligand + receptor) and then I submitted its trajectory frames
>> into the MM_PBSA.py script to obtain binding free energy value, am I in a
>> correct way? because in literatures I often saw that 3 MD simulations were
>> needed for this kind of calculations (i.e, ligand, receptor and complex).
>> I would be grateful for any advice from your site.
>> Sincerely,Berk
>>
>>
>>
>>
>>
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Received on Sat May 09 2015 - 04:30:02 PDT
