Hi George,
On Mon, Apr 25, 2011 at 4:53 AM, George Tzotzos <gtzotzos.me.com> wrote:
> Hi everybody,
>
> I've been trying to derive free energies of binding of a ligand (organic
> molecule), small protein complex following the procedure given in tutorial 3
> http://ambermd.org/tutorials/advanced/tutorial3/section1.htm
>
> My question is whether during minimisation, heating and density
> equilibration BOTH the ligand and protein should be restrained using the
> SAME restraint weight. The reason I'm asking this is that on a couple of
> occasions where I used restraints of the same weight (restraint_wt = 2.0) on
> both ligand and protein the ligand failed to move much from its original
> position.
>
I see no reason to use different restraint weights for each one, and that is
only possible via group input format (not restraint_wt and restraintmask).
As far as not seeing the system move much -- there is an 8 kcal/mol barrier
for *any* atom migrating 2 Å away from its starting position, and 2 kcal/mol
barrier for a *single* atom migrating 1 Å away, with this situation only
getting more severe as you travel farther away. restraint_wt=2.0 is still
quite strong if you wish to see any kind of mobility.
HTH,
Jason
> Many thanks on any advice on this matter
>
> Regards
>
> George
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Apr 25 2011 - 09:30:02 PDT
