Hi all,
I have done MD simulation using AMBER11. and now I am trying to calculate the Protein-Protein binding energy
using MMPBSA method.
Also i have enabled the entropy calculation (QUASI-HARMONIC APPROXIMATION).
But unfortunately, the entropy values were zero. what was the problem?
the command is:
MMPBSA.MPI -O -i mmpbsa_2.in -o Apo_MMPBSA_19_DS.dat -sp complex_wat.prmtop -cp complex_nowat.prmtop -rp protein1_nowat.prmtop -lp protein2_nowat.prmtop -y
../../md19.mdcrd.gz > mmpbsa.log &
the Input file and the results are:
|Input file:
|--------------------------------------------------------------
|Input file for running PB and GB
|&general
| endframe=50, verbose=1, receptor_mask= :1-331:744-745, ligand_mask=:332-743, entropy=1,
|/
|&gb
| igb=2, saltcon=0.100
|/
|&pb
| istrng=0.100,
|/
|
|--------------------------------------------------------------
|Solvated complex topology file: complex_wat.prmtop
|Complex topology file: complex_nowat.prmtop
|Receptor topology file: protein1_nowat.prmtop
|Ligand topology file: protein2_nowat.prmtop
|Initial mdcrd(s): ../../md18.mdcrd.gz
|
|Best guess for receptor mask: ":1-331:744-745"
|Best guess for ligand mask: ":332-743"
|Calculations performed using 50 frames.
|Poisson Boltzmann calculations performed using internal PBSA solver in sander.
|
|All units are reported in kcal/mole.
|All entropy results have units kcal/mole (Temperature is 298.15 K).
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
ENTROPY RESULTS (QUASI-HARMONIC APPROXIMATION) CALCULATED WITH PTRAJ:
Translational Rotational Vibrational Total
Complex: 0.0000 0.0000 0.0000 0.0000
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
why it gave an Entropy = 0 ?
I can provide the crd and prmtop files for you if it is necessary.
thank u
regards
BELAL OMAR AL NAJJAR
H/P: 0147462707
Pharmaceutical Design and Simulation Lab (PhDS)
Pharmaceutical Technology Department
School of Pharmaceutical Sciences
University of Science Malaysia
Penang
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Received on Mon Aug 01 2011 - 21:30:02 PDT
