Many thanks, Jason
I thought so.
All the best
George
On Apr 25, 2011, at 6:02 PM, Jason Swails wrote:
> 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
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Apr 25 2011 - 09:30:03 PDT
