Hello,
This is a very strange calculation. If I understand what you're trying to
do, you have a periodic box of water that you then apply MM/PBSA to,
treating the box of water as the receptor and glucose molecule as the
ligand. I don't think the Delta GBtot means what you think it means here.
It's going to be, roughly, the solvation energy of a box of water with the
glucose inside minus the solvation energy of the glucose molecule by itself
minus the solvation energy of the box of water without the glucose.
>From your email, it seems that you expect to get something like the
solvation energy of the glucose from this simulation, which is not what you
get here. If the model worked perfectly (which it obviously doesn't), I
would expect this approach to give you a "binding" energy in this case of 0,
since you're effectively calculating the free energy of taking a glucose
molecule out of water (explicit box) and putting it into water (implicit
continuum). However, using only a single trajectory gives you a water
trajectory with a small cavity where the glucose molecule was with the water
molecules aligned for its presence (so you will get some electrostatic
clashes arising from the lack of the glucose's point charge distribution).
I'd bet that you'd get closer to 0 if you used a separate trajectory for
just the pure water (same number of water molecules, obviously).
Your results make sense to me, but I don't think you're addressing the
problem you'd like to ask.
Hope this helps,
Jason
On Thu, Mar 24, 2011 at 6:02 PM, Hoshin Kim <85hskim.gmail.com> wrote:
> Dear all,
>
> I'm trying to calculate binding energy between glucose molecule and pure
> water by using AMBER 11 package. What I'm getting in trouble is GBtot has
> positive value (delta section in snap_statistics.out file). As you know,
> water interacts with glucose strongly, which means Binding energy should be
> negative value.
>
> There is single glucose molecule in TIP3P water box (625 molecules). and
> this simulation is 10ns simulation under NVT condition.
>
> Here belows are scripts which I've used,
>
> <<Taking snapshot>>
>
> PREFIX snap_
> PATH ./
> #
> COMPLEX 1
> RECEPTOR 1
> LIGAND 1
> #
> GC 1
> AS 0
> DC 0
> #
> MM 0
> GB 0
> PB 0
> MS 0
> #
> NM 0
> BOX YES
> NTOTAL 1899
> NSTART 1
> NSTOP 1
> NFREQ 1
> #
> NUMBER_LIG_GROUPS 1
> LSTART 1
> LSTOP 24
> NUMBER_REC_GROUPS 1
> RSTART 25
> RSTOP 1899
> .TRAJECTORY
> TRAJECTORY ./md_9999.x
>
> <MM_PBSA_GB>>
>
> PREFIX snap_
> PATH ./snapshot
> #
> COMPLEX 1
> RECEPTOR 1
> LIGAND 1
> #
> COMPT Lwatall.prmtop
> RECPT Lwatrest.prmtop
> LIGPT Lwat03.prmtop
> #
> GC 0
> AS 0
> DC 0
> #
> MM 1
> GB 1
> PB 0
> MS 1
> #
> NM 0
> .GB
> IGB 2
> GBSA 1
> SALTCON 0
> EXTDIEL 80.0
> INTDIEL 1.0
> #
> SURFTEN 0.0072
> SURFOFF 0.00
> .MS
> PROBE 0.0
> .MM
> DIELC 1.0
> .PB
> #PROC 2
> #REFE 0
> #INDI 1.0
> #EXDI 80.0
> #SCALE 2
> #LINIT 1000
> #PRBRAD 1.4
> #ISTRNG 0.0
> #RADIOPT 0
> #NPOPT 1
> #CAVITY_SURFTEN 0.0072
> #CAVITY_OFFSET 0.00
> #SURFTEN 0.0072
> #SURFOFF 0.00
>
>
> <Result>
>
> DELTA
> # -----------------------
> # MEAN STD
> # =======================
> ELE -21.06 11.89
> VDW -5.59 0.00
> INT 0.00 0.00
> GAS -26.65 11.89
> GBSUR 0.00 0.00
> GB 40.26 22.94
> GBSOL 40.26 22.94
> GBELE 19.20 11.06
> *GBTOT 13.61 11.06*
> *
> *
> Could anyone give me an advice to figure it out ?
>
>
> Thanks you in advance.
>
> Hoshin Kim
> _______________________________________________
> 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
Received on Thu Mar 24 2011 - 19:00:02 PDT
