Were any GB of PB calculations performed? For the entropy calculations in
particular, you should check out the _MMPBSA_complex_entropy.out,
_MMPBSA_receptor_entropy.out, and _MMPBSA_ligand_entropy.out files. Those
files are the corresponding output files for the entropy calculation.
Ideally there will be helpful information in those files that would point to
the source of the problem.
-Bill
On Tue, Aug 2, 2011 at 12:25 AM, belal najjar <belalnajjar.yahoo.com> wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Tue Aug 02 2011 - 04:00:03 PDT
