AMBER: A problem with mm_pbsa

From: <vic.mail.nankai.edu.cn>
Date: Tue, 26 Dec 2006 09:41:41 +0800

Hi,

I use mm_pbsa to get the binding energy, there are lots of WARNINGs, and the out
put is not good, because the STD is to high.

Is there anybody who can tell me what is wrong.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
=>> Reading files
    Reading purp_com.all.out
    Reading purp_rec.all.out
    Checking CALC
    WARNING: Missing PBCAV for PB in 2 -> Taken from 1
    WARNING: Missing PBDIS for PB in 2 -> Taken from 1
    WARNING: Missing SURF for MS in 2 -> Taken from 1
    WARNING: Missing PBCAV for PB in 41 -> Taken from 40
    WARNING: Missing PBDIS for PB in 41 -> Taken from 40
    WARNING: Missing SURF for MS in 41 -> Taken from 40
    WARNING: Missing PBCAV for PB in 81 -> Taken from 80
    WARNING: Missing PBDIS for PB in 81 -> Taken from 80
    WARNING: Missing SURF for MS in 81 -> Taken from 80
    WARNING: Missing PBCAV for PB in 84 -> Taken from 83
    WARNING: Missing PBDIS for PB in 84 -> Taken from 83
    WARNING: Missing SURF for MS in 84 -> Taken from 83
    WARNING: Missing PBCAV for PB in 96 -> Taken from 95
    WARNING: Missing PBDIS for PB in 96 -> Taken from 95
    WARNING: Missing SURF for MS in 96 -> Taken from 95
    Reading purp_lig.all.out
    Checking CALC
    WARNING: Missing PB for PB in 0 -> Taken from -1
    WARNING: Missing PB for PB in 1 -> Taken from 0
    WARNING: Missing PB for PB in 2 -> Taken from 1
    WARNING: Missing PB for PB in 3 -> Taken from 2
    WARNING: Missing PB for PB in 4 -> Taken from 3
    WARNING: Missing PB for PB in 5 -> Taken from 4
    WARNING: Missing PB for PB in 6 -> Taken from 5
    WARNING: Missing PB for PB in 7 -> Taken from 6
    WARNING: Missing PB for PB in 8 -> Taken from 7
    WARNING: Missing PB for PB in 9 -> Taken from 8
    WARNING: Missing PB for PB in 10 -> Taken from 9
    WARNING: Missing PB for PB in 11 -> Taken from 10
    WARNING: Missing PB for PB in 12 -> Taken from 11
    WARNING: Missing PB for PB in 13 -> Taken from 12
    WARNING: Missing PB for PB in 14 -> Taken from 13
    WARNING: Missing PB for PB in 15 -> Taken from 14
    WARNING: Missing PB for PB in 16 -> Taken from 15
    WARNING: Missing PB for PB in 17 -> Taken from 16
    WARNING: Missing PB for PB in 18 -> Taken from 17
    WARNING: Missing PB for PB in 19 -> Taken from 18
    WARNING: Missing PB for PB in 20 -> Taken from 19
    WARNING: Missing PB for PB in 21 -> Taken from 20
    WARNING: Missing PB for PB in 22 -> Taken from 21
    WARNING: Missing PB for PB in 23 -> Taken from 22
    WARNING: Missing PB for PB in 24 -> Taken from 23
    WARNING: Missing PB for PB in 25 -> Taken from 24
    WARNING: Missing PB for PB in 26 -> Taken from 25
    WARNING: Missing PB for PB in 27 -> Taken from 26
    WARNING: Missing PB for PB in 28 -> Taken from 27
    WARNING: Missing PB for PB in 29 -> Taken from 28
    WARNING: Missing PB for PB in 30 -> Taken from 29
    WARNING: Missing PB for PB in 31 -> Taken from 30
    WARNING: Missing PB for PB in 32 -> Taken from 31
    WARNING: Missing PB for PB in 33 -> Taken from 32
    WARNING: Missing PB for PB in 34 -> Taken from 33
    WARNING: Missing PB for PB in 35 -> Taken from 34
    WARNING: Missing PB for PB in 36 -> Taken from 35
    WARNING: Missing PB for PB in 37 -> Taken from 36
    WARNING: Missing PB for PB in 38 -> Taken from 37
    WARNING: Missing PB for PB in 39 -> Taken from 38
    WARNING: Missing PB for PB in 40 -> Taken from 39
    WARNING: Missing PB for PB in 41 -> Taken from 40
    WARNING: Missing PB for PB in 42 -> Taken from 41
    WARNING: Missing PB for PB in 43 -> Taken from 42
    WARNING: Missing PB for PB in 44 -> Taken from 43
    WARNING: Missing PB for PB in 45 -> Taken from 44
    WARNING: Missing PB for PB in 46 -> Taken from 45
    WARNING: Missing PB for PB in 47 -> Taken from 46
    WARNING: Missing PB for PB in 48 -> Taken from 47
    WARNING: Missing PB for PB in 49 -> Taken from 48
    WARNING: Missing PB for PB in 50 -> Taken from 49
    WARNING: Missing PB for PB in 51 -> Taken from 50
    WARNING: Missing PB for PB in 52 -> Taken from 51
    WARNING: Missing PB for PB in 53 -> Taken from 52
    WARNING: Missing PB for PB in 54 -> Taken from 53
    WARNING: Missing PB for PB in 55 -> Taken from 54
    WARNING: Missing PB for PB in 56 -> Taken from 55
    WARNING: Missing PB for PB in 57 -> Taken from 56
    WARNING: Missing PB for PB in 58 -> Taken from 57
    WARNING: Missing PB for PB in 59 -> Taken from 58
    WARNING: Missing PB for PB in 60 -> Taken from 59
    WARNING: Missing PB for PB in 61 -> Taken from 60
    WARNING: Missing PB for PB in 62 -> Taken from 61
    WARNING: Missing PB for PB in 63 -> Taken from 62
    WARNING: Missing PB for PB in 64 -> Taken from 63
    WARNING: Missing PB for PB in 65 -> Taken from 64
    WARNING: Missing PB for PB in 66 -> Taken from 65
    WARNING: Missing PB for PB in 67 -> Taken from 66
    WARNING: Missing PB for PB in 68 -> Taken from 67
    WARNING: Missing PB for PB in 69 -> Taken from 68
    WARNING: Missing PB for PB in 70 -> Taken from 69
    WARNING: Missing PB for PB in 71 -> Taken from 70
    WARNING: Missing PB for PB in 72 -> Taken from 71
    WARNING: Missing PB for PB in 73 -> Taken from 72
    WARNING: Missing PB for PB in 74 -> Taken from 73
    WARNING: Missing PB for PB in 75 -> Taken from 74
    WARNING: Missing PB for PB in 76 -> Taken from 75
    WARNING: Missing PB for PB in 77 -> Taken from 76
    WARNING: Missing PB for PB in 78 -> Taken from 77
    WARNING: Missing PB for PB in 79 -> Taken from 78
    WARNING: Missing PB for PB in 80 -> Taken from 79
    WARNING: Missing PB for PB in 81 -> Taken from 80
    WARNING: Missing PB for PB in 82 -> Taken from 81
    WARNING: Missing PB for PB in 83 -> Taken from 82
    WARNING: Missing PB for PB in 84 -> Taken from 83
    WARNING: Missing PB for PB in 85 -> Taken from 84
    WARNING: Missing PB for PB in 86 -> Taken from 85
    WARNING: Missing PB for PB in 87 -> Taken from 86
    WARNING: Missing PB for PB in 88 -> Taken from 87
    WARNING: Missing PB for PB in 89 -> Taken from 88
    WARNING: Missing PB for PB in 90 -> Taken from 89
    WARNING: Missing PB for PB in 91 -> Taken from 90
    WARNING: Missing PB for PB in 92 -> Taken from 91
    WARNING: Missing PB for PB in 93 -> Taken from 92
    WARNING: Missing PB for PB in 94 -> Taken from 93
    WARNING: Missing PB for PB in 95 -> Taken from 94
    WARNING: Missing PB for PB in 96 -> Taken from 95
    WARNING: Missing PB for PB in 97 -> Taken from 96
    WARNING: Missing PB for PB in 98 -> Taken from 97
    WARNING: Missing PB for PB in 99 -> Taken from 98
    WARNING: Missing PB for PB in 100 -> Taken from 99
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


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Received on Wed Dec 27 2006 - 06:07:39 PST
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