Dear Jason
Thanks for your answer.
Based on your suggestion, I tried MMPBSA.py. I have no problem.
But, I have some general question:
1) Should I use all of the frames in solvated complex trajectory? Binding
delta G is different in various selections of frames. Is there a criterion
for selection of frames for MM-PBSA and MM-GBSA calculation (startframe and
endframe)? I have 2000 frames, what is your suggestion?
2) I calculated the binding free energy of my complex (protein-ligand) +
Quasi-harmonic entropy for one frame of trajectory:
Energy Component Average
--------------------------------------------
BOND -0.0001
ANGLE 0.0000
DIHED -0.0000
VDWAALS -22.8383
EEL -6.8608
1-4 VDW 0.0001
1-4 EEL -0.0000
EPB 18.8155
ENPOLAR -15.1933
EDISPER 23.7355
DELTA G gas -29.6991
DELTA G solv 27.3577
DELTA TOTAL -2.3414
-------------------------------------------------------------------------------
Using Quasi-harmonic Entropy Approximation: DELTA G binding = 18.4960
-------------------------------------------------------------------------------
Since 1- Delta G = Delta H - T * Delta S and 2- Temperature is 298.15 K in
this calculation, thus
18.4960 = -2.3414 - 298.15 * Delta S, ===> Delta S = 0.069 kcal/mol.K
Is my consideration true?
3) I calculated 1- the binding free energy of my complex (protein-ligand)
for one frame of trajectory and 2- I calculated entropy of my complex
(protein-ligand) using Normal Mode Analysis for the same frame:
Energy Component Average
----------------------------------------------
BOND -0.0001
ANGLE 0.0000
DIHED -0.0000
VDWAALS -22.8383
EEL -6.8608
1-4 VDW 0.0001
1-4 EEL -0.0000
EPB 18.8155
ENPOLAR -15.1933
EDISPER 23.7355
DELTA G gas -29.6991
DELTA G solv 27.3577
DELTA TOTAL -2.3414
Entropy Term Average
----------------------------------------------
Translational -12.1100
Rotational -8.7200
Vibrational 17.2921
DELTA S total= -3.5378
There are following in output file:
All units are reported in kcal/mole.
All entropy results have units kcal/mol (Temperature is 298.15 K).
How to use and combine DELTA S total (-3.5378) with DELTA TOTAL (-2.3414)?
Delta G = Delta H - T * Delta S
Delta G = (-2.3414) - (-3.5378)
Is my consideration true?
Best wishes,
Atila
On Wed, Mar 4, 2015 at 4:13 PM, Jason Swails <jason.swails.gmail.com> wrote:
>
> > On Mar 4, 2015, at 2:49 AM, Atila Petrosian <atila.petrosian.gmail.com>
> wrote:
> >
> > Dear amber users
> >
> > I am doing MM-PBSA calculation for my protein-ligand system based on
> TUTORIAL
> > A3: MM-PBSA <http://ambermd.org/tutorials/advanced/tutorial3/index.htm>
> > using AmberTools 14.
> >
> > I encountered a problem in section 3 of this tutorial:
> >
> > http://ambermd.org/tutorials/advanced/tutorial3/section3.htm
> >
> > After successfully extracting of snapshots, I prepared input file (
> > binding_energy.mmpbsa).
> >
> --------------------------------------------------------------------------------------------------
> > .GENERAL
> > VERBOSE 0
> > PARALLEL 0
> > PREFIX snapshot
> > PATH ./
> > START 200
> > STOP 300
> > OFFSET 1
> > COMPLEX 1
> > RECEPTOR 1
> > LIGAND 1
> > COMPT ./comp1.prmtop
> > RECPT ./hsa1.prmtop
> > LIGPT ./sal1_h.prmtop
> > GC 0
> > AS 0
> > DC 0
> > MM 1
> > GB 1
> > PB 1
> > MS 1
> > NM 1
> > .PB
> > PROC 2
> > REFE 0
> > INDI 1.0
> > EXDI 80.0
> > SCALE 5
> > LINIT 1000
> > PRBRAD 1.4
> > ISTRNG 0.0
> > RADIOPT 0
> > NPOPT 1
> > ARCRES 0.0625
> > INP 1
> > SURFTEN 0.005
> > SURFOFF 0.00
> > IVCAP 0
> > CUTCAP -1.0
> > XCAP 0.0
> > YCAP 0.0
> > ZCAP 0.0
> > .MM
> > DIELC 1.0
> > .GB
> > IGB 2
> > GBSA 1
> > SALTCON 0.00
> > EXTDIEL 80.0
> > INTDIEL 1.0
> > SURFTEN 0.005
> > SURFOFF 0.00
> > .MS
> > PROBE 0.0
> > .NM
> > DIELC 4
> > MAXCYC 1000
> > DRMS 0.1
> > .PROGRAMS
> >
> --------------------------------------------------------------------------------------------------
> > Then I used this command:
> >
> > $AMBERHOME/bin/mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log
> >
> > But I get following:
> >
> > Param PROC does not exist
> > For details see:
> > http://ambermd.org/Questions/mm_pbsa.html#testpar_param_not_existent
> >
> > How to resolve this problem?
>
> Maybe you need to add the PROC keyword to the NM section? See the manual
> for details. If that doesn’t work, I would suggest trying MMPBSA.py
> instead (also in Tutorial 3). That version is typically better-supported
> on the mailing list.
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Mar 05 2015 - 09:00:02 PST
