Dear prof. Case,
thank you very much for your valuable reply !
Regarding the scripts, they are just small modifications of the Thomas's
one from tut. A9
(i.e. this:
http://ambermd.org/tutorials/advanced/tutorial9/prepare_example.bat ).
It seemed to me also a bit complicated on the first sight but then I found
it pretty useful
as it prepare all the necessary files automatically and if you want to
change some parameter
you do tis just here in this script.
You are right, I did not use softcore potential for electrostatic
decoupling of the phenol
from the water (this I used only in case of vdw decoup.) as neither Thomas
used it in his tutorial.
I repeated my calculation of dG_bulk_elec of phenol with softcore
potential and obtained value -6.06 kcal/mol
which is in good agreement with value from the Roux article (-6.03
kcal/mol). After reminding of some relevant parts from Amber11 manual
I also tested "One Step" (soft vdw and soft el. potential) approach to
decouple benzene from water and obtained reasonable result of solvation
free
energy (-0.75 kacl/mol) considering experimental value (-0.87 kcal/mol)
and just 0.1 to 0.9 lambdas with simple integration method.
So if I understood well if one uses simple linear mixing without softcore
potential in case of electrostatic
decoupling, all el. interactions of the ligand with it's surrounding BUT
ALSO THE INTERNAL ONES (between atoms of the ligand)
are gradually turned off so if one would like to obtain full solvation
energy he must add additional step to compute energy
associated with reappearing of the internal electrostatic interactions of
the ligand in vacuum.
On the other hand if one uses softcore potential for this step, the
internal electrostatic interactions of the ligand
are unchanged during the decoupling process (similarily like in vdw case)
so there is no need to do vacuum step.
Am I right or I did not understand it properly ?
Best wishes,
Marek
Dne Sat, 05 May 2012 15:45:09 +0200 case <case.biomaps.rutgers.edu>
napsal/-a:
> On Wed, May 02, 2012, Marek Maly wrote:
>
>> I repeated calculation of dG_bulk_elec of phenol using input files from
>> tut. A9 and have obtained value -38.49138 kcal/mol which is almost
>> identical with the previously reported value ( -38.64 see below) which
>> is really different from the value reported in below mentioned article (
>> -6.03 kcal/mol).
>
> If dG_bulk_elec refers to phenol in bulk water, then this number is way
> wrong
> (as you point out). It was kind of hard to follow the scripts to
> supplied,
> but I don't see where you are computing the electrostatic change in
> vacuum:
> this needs to be subtracted from the charging free energy in water to
> get the
> electrostatic contribution to the solvation free energy.
>
> [The "softcore" code makes this vaccum step unnecessary, but you don't
> seem
> to be using that option(?)]
>
> ...hope this helps....dac
>
>
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Received on Sun May 06 2012 - 09:30:03 PDT
