[AMBER] MM_PBSA: abnormal VDW interaction energy

From: LIU Huanxiang <liuhx1003.yahoo.com.cn>
Date: Tue, 6 Oct 2009 10:43:21 +0800 (CST)

Dear Sir,
    When I use mm_pbsa to calculate the binding energy, I obtained one abnormal results. The binding free energy is -6563.33  and -6566.00 from mm_pbsa and mm_gbsa, respectively. The detailed results were given as follows. From the analysis of obtained results, I found there are some problems of the calculation of  VDW interaction. But for another system, I can obtain the correct results.  I don't know what will result in this phenomenon. Could you give me some sugestions? Thanks a lot!
 
Best regards
Sincerely yours
Xiang
 
#                  COMPLEX                RECEPTOR                  LIGAND
#          ----------------------- ----------------------- -----------------------
#                  MEAN        STD         MEAN        STD         MEAN        STD
#          ======================= ======================= =======================
ELE             -10198.84      73.96     -9459.89      70.48      -398.67       9.87
VDW            -1828.25      30.59      4686.12     600.89         9.12       3.33
INT             8237.13      53.79      8105.42      52.94       100.66       8.49
GAS            -3789.97      83.19      3331.66     608.29      -288.88       7.11
PBSUR            104.27       0.99       105.32       0.95         3.88       0.03
PBCAL          -2814.21      55.59     -2927.07      53.21      -161.48       4.27
PBSOL          -2709.94      55.29     -2821.75      52.87      -157.60       4.26
PBELE         -13013.05      38.02    -12386.96      36.75      -560.15       8.98
PBTOT          -6499.91      56.38       509.90     605.51      -446.48       4.76
GBSUR            104.27       0.99       105.32       0.95         3.88       0.03
GB             -2966.35      58.43     -3084.64      56.22      -153.39       4.24
GBSOL          -2862.08      58.13     -2979.32      55.87      -149.51       4.23
GBELE         -13165.19      32.04    -12544.53      29.95      -552.05       8.19
GBTOT          -6652.05      55.03       352.34     604.65      -438.39       4.97
#                    DELTA
#          -----------------------
#                  MEAN        STD
#          =======================
ELE             -340.29      19.99
VDW            -6523.49     601.43
INT               31.04       2.55
GAS            -6832.74     601.79
PBSUR             -4.93       0.12
PBCAL            274.34      13.02
PBSOL            269.41      13.06
PBELE            -65.95      10.28
PBTOT          -6563.33     600.87
GBSUR             -4.93       0.12
GB               271.67      12.90
GBSOL            266.74      12.95
GBELE            -68.62       9.87
GBTOT          -6566.00     601.10 ___________________________________________________________ 好玩贺卡等你发,邮箱贺卡全新上线! http://card.mail.cn.yahoo.com/
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Received on Mon Oct 05 2009 - 20:00:02 PDT
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