Hi Thomas,
if I understood well in Amber11 if one would like to calculate dG of
decoupling
of ligand from receptor using proper restraint it is enough to set
parameter dvdl_norest = 1
(to prevent including restraint contribution to dV/dl) and that.s all ?
Best wishes,
Marek
Dne Thu, 05 Jan 2012 10:49:15 +0100 <steinbrt.rci.rutgers.edu> napsal/-a:
> Hi,
>
>> So this set up still no ligand in V1 state. Can you kindly explain why
>> you
>> think still maintains ligand internal potentials? I thought this ligand
>
> Because that's the way I wrote the code. Any bonded interaction involving
> at least one atom in scmask is made non-lambda dependent, does not
> contribute to dvdl and remains unchanged. I think that is what you would
> want the behaviour to be in almost any TI calculation.
>
>> Another question is about dvdl_norest, in this kind free energy
>> calculation, we usually need restraint the ligand around origin
>> position (
>> in protein binding site). So I thought we need set this parameter to no.
>> But how to correct this restraint later on?
>
> dvdl_norest does not set or change restraints, it only makes them not
> count for dvdl, basically treating them like a bonded interaction of the
> ligand. This isn't done automatically because it depends on your
> calculation setup if you want this potential counted or not. You still
> have to set the restraints yourself (and maybe scale them depending on
> lambda)
>
> In the case of:
>
> V0: Protein+Ligand+Ligand_restraint+Water
>
> V1: Protein+Water
>
> we want to set scmask (on V0) to 'Ligand' and dvdl_norest to 'on'. Then
> the transformation is equivalent to decoupling the ligand but keeping its
> internal potentials and restraint unchanged and not contributing to dvdl.
>
> On additional difficulty is: Since the restraint makes only sense to
> define on process 0, it automatically becomes scaled by lambda and we
> dont
> want that. I believe that, as of Amber11, the code automatically corrects
> this for you, but check the manual on that.
>
> Kind Regards,
>
> Thomas
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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Received on Fri Jan 06 2012 - 08:30:03 PST
