[AMBER] FINAL_RESULTS_MMPBSA error

From: filip fratev <filipfratev.yahoo.com>
Date: Thu, 19 Dec 2013 23:23:41 -0800 (PST)

Hi all, When I use only &pb in my MMPBSA calculations I obtain a reasonable value for EPB, but when I set idecomp=3 the EPB was about 10x smaller in the final_result_mmpbsa file (EPB   67.5297 ). I used the same input files and all other energies are indeed identical. Is that a bug? May I consider that the decomposition energies are correct? Regards, Filip FINAL_RESULTS_MMPBSA error: Input file: |-------------------------------------------------------------- |Input file for running PB and GB |&general |startframe=8001, endframe=10000, interval=25, strip_mask=":WAT,Cl-", verbose=1, |#  entropy=1, |/ |#&gb |#  igb=2, saltcon=0.100 |#/ |&pb |  istrng=0.100, |/ |#&decomp |#  idecomp=3, print_res="68-73; 59-67; 74-96; 107-130; 157-167" |#  dec_verbose=1, |#/ |#&rism |#  polardecomp=1, thermo='gf'-------------------------------------------------------------- |MMPBSA.py Version=13.0 |Solvated complex topology file:  2IOG.prmtop |Complex topology file:           complex.prmtop |Receptor topology file:          receptor.prmtop |Ligand topology file:            ligand.prmtop |Initial mdcrd(s):                ProdER.mdcrd | |Receptor mask:                  ":1-96" |Ligand mask:                    ":97-181" | |Calculations performed using 80 complex frames. |Poisson Boltzmann calculations performed using internal PBSA solver in mmpbsa_py_energy | |All units are reported in kcal/mole. ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- POISSON BOLTZMANN: Complex: Energy Component            Average              Std. Dev.   Std. Err. of Mean ------------------------------------------------------------------------------- VDWAALS                  -1300.4345               18.8683              2.1095 EEL                     -12945.1069               74.5359              8.3334 EPB                      -1914.8786               63.0355              7.0476 ENPOLAR                   1402.5128                8.0609              0.9012 EDISPER                   -873.7300                9.5301              1.0655 G gas                   -14245.5414               71.0483              7.9434 G solv                   -1386.0958               61.4583              6.8712 TOTAL                   -15631.6372               37.8815              4.2353 Receptor: Energy Component            Average              Std. Dev.   Std. Err. of Mean ------------------------------------------------------------------------------- VDWAALS                   -636.0225               14.8670              1.6622 EEL                      -6543.5816               59.8964              6.6966 EPB                      -1447.8124               53.1049              5.9373 ENPOLAR                    785.3782                7.4245              0.8301 EDISPER                   -537.1198               10.6839              1.1945 G gas                    -7179.6041               60.2133              6.7321 G solv                   -1199.5540               53.9111              6.0274 TOTAL                    -8379.1581               30.2407              3.3810 Ligand: Energy Component            Average              Std. Dev.   Std. Err. of Mean ------------------------------------------------------------------------------- VDWAALS                   -561.7187               10.8015              1.2076 EEL                      -5654.4483               52.6886              5.8908 EPB                      -1220.6693               35.1604              3.9311 ENPOLAR                    699.3572                5.2038              0.5818 EDISPER                   -481.4802                5.2586              0.5879 G gas                    -6216.1670               52.5901              5.8797 G solv                   -1002.7923               33.8162              3.7808 TOTAL                    -7218.9593               37.4935              4.1919 Differences (Complex - Receptor - Ligand): Energy Component            Average              Std. Dev.   Std. Err. of Mean ------------------------------------------------------------------------------- VDWAALS                   -102.6933                5.4243              0.6065 EEL                       -747.0770               35.9132              4.0152 EPB                        753.6030               33.1830              3.7100 ENPOLAR                    -82.2225                3.7455              0.4188 EDISPER                    144.8700                4.5622              0.5101 DELTA G gas               -849.7703               36.6566              4.0983 DELTA G solv               816.2504               33.6160              3.7584 DELTA TOTAL                -33.5198               10.8837              1.2168 ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- nput file for running PB and GB |&general |startframe=8001, endframe=10000, interval=25, strip_mask=":WAT,Cl-", verbose=1, |#  entropy=1, |/ |#&gb |#  igb=2, saltcon=0.100 |#/ |&pb |  istrng=0.100, |/ |&decomp |  idecomp=3, print_res="68-73; 59-67; 74-96; 107-130; 157-167" |  dec_verbose=1, |#/ |#&rism |#  polardecomp=1, thermo='gf'-------------------------------------------------------------- |MMPBSA.py Version=13.0 |Solvated complex topology file:  2IOG.prmtop |Complex topology file:           complex.prmtop |Receptor topology file:          receptor.prmtop |Ligand topology file:            ligand.prmtop |Initial mdcrd(s):                ProdER.mdcrd | |Receptor mask:                  ":1-96" |Ligand mask:                    ":97-181" | |Calculations performed using 80 complex frames. |Poisson Boltzmann calculations performed using internal PBSA solver in sander. | |All units are reported in kcal/mole. ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- POISSON BOLTZMANN: Complex: Energy Component            Average              Std. Dev.   Std. Err. of Mean ------------------------------------------------------------------------------- VDWAALS                  -1300.4345               18.8683              2.1095 EEL                     -12945.1069               74.5359              8.3334 EPB                        -53.3041                8.6451              0.9666 ENPOLAR                   1402.5128                8.0609              0.9012 EDISPER                   -873.7300                9.5301              1.0655 G gas                   -14245.5414               71.0483              7.9434 G solv                     475.4787               10.1290              1.1325 TOTAL                   -13770.0627               70.6477              7.8986 Receptor: Energy Component            Average              Std. Dev.   Std. Err. of Mean ------------------------------------------------------------------------------- VDWAALS                   -636.0225               14.8670              1.6622 EEL                      -6543.5816               59.8964              6.6966 EPB                        -40.3898               10.5803              1.1829 ENPOLAR                    785.3782                7.4245              0.8301 EDISPER                   -537.1198               10.6839              1.1945 G gas                    -7179.6041               60.2133              6.7321 G solv                     207.8686               11.9526              1.3363 TOTAL                    -6971.7355               57.7394              6.4555 Ligand: Energy Component            Average              Std. Dev.   Std. Err. of Mean ------------------------------------------------------------------------------- VDWAALS                   -561.7187               10.8015              1.2076 EEL                      -5654.4483               52.6886              5.8908 EPB                        -80.4440                9.0166              1.0081 ENPOLAR                    699.3572                5.2038              0.5818 EDISPER                   -481.4802                5.2586              0.5879 G gas                    -6216.1670               52.5901              5.8797 G solv                     137.4330                8.9145              0.9967 TOTAL                    -6078.7340               51.8037              5.7918 Differences (Complex - Receptor - Ligand): Energy Component            Average              Std. Dev.   Std. Err. of Mean ------------------------------------------------------------------------------- VDWAALS                   -102.6933                5.4243              0.6065 EEL                       -747.0770               35.9132              4.0152 EPB                         67.5297               11.5401              1.2902 ENPOLAR                    -82.2225                3.7455              0.4188 EDISPER                    144.8700                4.5622              0.5101 DELTA G gas               -849.7703               36.6566              4.0983 DELTA G solv               130.1771               11.4431              1.2794 DELTA TOTAL               -719.5931               37.1032              4.1483 ------------------------------------------------------------------------------- -------------------------------------------------------------------------------

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Received on Thu Dec 19 2013 - 23:30:02 PST
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