This is an addition to the email sent on Sat, Feb 9. Unfortunately I
did not receive the response of Daniel Roe, so I am unsure how to
continue that thread.
I am simulating the pKa of residue in a protein, and I wish to know in
what manner each residue is contributing to energy changes. My input
file is as follows:
&cntrl
nstlim =1, nscm=2000,
ntx=1, irest=0, ntpr=1000,
tempi=300.0, temp0=300.0, ntt=3, gamma_ln=5.0,
ntb=0, igb=5, cut=999.0,
dt=0.001,
idecomp=1,
ntc=2, ntf=2,
ntwr = 10000, ntwx=1000, ntave=1000
/
All Residues
RES -1 124
END
END
My relevant output is as follows
LOADING THE DECOMP ATOMS AS GROUPS
----- READING GROUP 1; TITLE:
All Residues
GROUP 1 CONSISTS OF RESIDUE 1
GROUP 2 CONSISTS OF RESIDUE 2
GROUP 3 CONSISTS OF RESIDUE 3
GROUP 4 CONSISTS OF RESIDUE 4
GROUP 5 CONSISTS OF RESIDUE 5
GROUP 6 CONSISTS OF RESIDUE 6
GROUP 7 CONSISTS OF RESIDUE 7
GROUP 8 CONSISTS OF RESIDUE 8
GROUP 9 CONSISTS OF RESIDUE 9
GROUP 10 CONSISTS OF RESIDUE 10
GROUP 11 CONSISTS OF RESIDUE 11
GROUP 12 CONSISTS OF RESIDUE 12
GROUP 13 CONSISTS OF RESIDUE 13
GROUP 14 CONSISTS OF RESIDUE 14
GROUP 15 CONSISTS OF RESIDUE 15
GROUP 16 CONSISTS OF RESIDUE 16
GROUP 17 CONSISTS OF RESIDUE 17
GROUP 18 CONSISTS OF RESIDUE 18
GROUP 19 CONSISTS OF RESIDUE 19
GROUP 20 CONSISTS OF RESIDUE 20
GROUP 21 CONSISTS OF RESIDUE 21
GROUP 22 CONSISTS OF RESIDUE 22
GROUP 23 CONSISTS OF RESIDUE 23
GROUP 24 CONSISTS OF RESIDUE 24
GROUP 25 CONSISTS OF RESIDUE 25
GROUP 26 CONSISTS OF RESIDUE 26
GROUP 27 CONSISTS OF RESIDUE 27
GROUP 28 CONSISTS OF RESIDUE 28
GROUP 29 CONSISTS OF RESIDUE 29
GROUP 30 CONSISTS OF RESIDUE 30
GROUP 31 CONSISTS OF RESIDUE 31
GROUP 32 CONSISTS OF RESIDUE 32
GROUP 33 CONSISTS OF RESIDUE 33
GROUP 34 CONSISTS OF RESIDUE 34
GROUP 35 CONSISTS OF RESIDUE 35
GROUP 36 CONSISTS OF RESIDUE 36
GROUP 37 CONSISTS OF RESIDUE 37
GROUP 38 CONSISTS OF RESIDUE 38
GROUP 39 CONSISTS OF RESIDUE 39
GROUP 40 CONSISTS OF RESIDUE 40
GROUP 41 CONSISTS OF RESIDUE 41
GROUP 42 CONSISTS OF RESIDUE 42
GROUP 43 CONSISTS OF RESIDUE 43
GROUP 44 CONSISTS OF RESIDUE 44
GROUP 45 CONSISTS OF RESIDUE 45
GROUP 46 CONSISTS OF RESIDUE 46
GROUP 47 CONSISTS OF RESIDUE 47
GROUP 48 CONSISTS OF RESIDUE 48
GROUP 49 CONSISTS OF RESIDUE 49
GROUP 50 CONSISTS OF RESIDUE 50
GROUP 51 CONSISTS OF RESIDUE 51
GROUP 52 CONSISTS OF RESIDUE 52
GROUP 53 CONSISTS OF RESIDUE 53
GROUP 54 CONSISTS OF RESIDUE 54
GROUP 55 CONSISTS OF RESIDUE 55
GROUP 56 CONSISTS OF RESIDUE 56
GROUP 57 CONSISTS OF RESIDUE 57
GROUP 58 CONSISTS OF RESIDUE 58
GROUP 59 CONSISTS OF RESIDUE 59
GROUP 60 CONSISTS OF RESIDUE 60
GROUP 61 CONSISTS OF RESIDUE 61
GROUP 62 CONSISTS OF RESIDUE 62
GROUP 63 CONSISTS OF RESIDUE 63
GROUP 64 CONSISTS OF RESIDUE 64
GROUP 65 CONSISTS OF RESIDUE 65
GROUP 66 CONSISTS OF RESIDUE 66
GROUP 67 CONSISTS OF RESIDUE 67
GROUP 68 CONSISTS OF RESIDUE 68
GROUP 69 CONSISTS OF RESIDUE 69
GROUP 70 CONSISTS OF RESIDUE 70
GROUP 71 CONSISTS OF RESIDUE 71
GROUP 72 CONSISTS OF RESIDUE 72
GROUP 73 CONSISTS OF RESIDUE 73
GROUP 74 CONSISTS OF RESIDUE 74
GROUP 75 CONSISTS OF RESIDUE 75
GROUP 76 CONSISTS OF RESIDUE 76
GROUP 77 CONSISTS OF RESIDUE 77
GROUP 78 CONSISTS OF RESIDUE 78
GROUP 79 CONSISTS OF RESIDUE 79
GROUP 80 CONSISTS OF RESIDUE 80
GROUP 81 CONSISTS OF RESIDUE 81
GROUP 82 CONSISTS OF RESIDUE 82
GROUP 83 CONSISTS OF RESIDUE 83
GROUP 84 CONSISTS OF RESIDUE 84
GROUP 85 CONSISTS OF RESIDUE 85
GROUP 86 CONSISTS OF RESIDUE 86
GROUP 87 CONSISTS OF RESIDUE 87
GROUP 88 CONSISTS OF RESIDUE 88
GROUP 89 CONSISTS OF RESIDUE 89
GROUP 90 CONSISTS OF RESIDUE 90
GROUP 91 CONSISTS OF RESIDUE 91
GROUP 92 CONSISTS OF RESIDUE 92
GROUP 93 CONSISTS OF RESIDUE 93
GROUP 94 CONSISTS OF RESIDUE 94
GROUP 95 CONSISTS OF RESIDUE 95
GROUP 96 CONSISTS OF RESIDUE 96
GROUP 97 CONSISTS OF RESIDUE 97
GROUP 98 CONSISTS OF RESIDUE 98
GROUP 99 CONSISTS OF RESIDUE 99
GROUP 100 CONSISTS OF RESIDUE 100
GROUP 101 CONSISTS OF RESIDUE 101
GROUP 102 CONSISTS OF RESIDUE 102
GROUP 103 CONSISTS OF RESIDUE 103
GROUP 104 CONSISTS OF RESIDUE 104
GROUP 105 CONSISTS OF RESIDUE 105
GROUP 106 CONSISTS OF RESIDUE 106
GROUP 107 CONSISTS OF RESIDUE 107
GROUP 108 CONSISTS OF RESIDUE 108
GROUP 109 CONSISTS OF RESIDUE 109
GROUP 110 CONSISTS OF RESIDUE 110
GROUP 111 CONSISTS OF RESIDUE 111
GROUP 112 CONSISTS OF RESIDUE 112
GROUP 113 CONSISTS OF RESIDUE 113
GROUP 114 CONSISTS OF RESIDUE 114
GROUP 115 CONSISTS OF RESIDUE 115
GROUP 116 CONSISTS OF RESIDUE 116
GROUP 117 CONSISTS OF RESIDUE 117
GROUP 118 CONSISTS OF RESIDUE 118
GROUP 119 CONSISTS OF RESIDUE 119
GROUP 120 CONSISTS OF RESIDUE 120
GROUP 121 CONSISTS OF RESIDUE 121
GROUP 122 CONSISTS OF RESIDUE 122
GROUP 123 CONSISTS OF RESIDUE 123
GROUP 124 CONSISTS OF RESIDUE 124
Number of atoms in this group = 1857
----- READING GROUP 125; TITLE:
END
rfree: End of file on unit 5
It appears that instead of interpreting my second END as the end of the
group specification, it interprets it as the title of the next group.
Any suggestions?
Sincerely,
Adam Mepham
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Received on Mon Feb 11 2013 - 14:30:04 PST
