ADL: Problem with dlg file

anna duraj annaduraj at gmail.com
Wed Feb 20 10:06:25 PST 2008


Hi all,

I am running Autodock 4.0 and I am getting dlg.file but this file gives me
error :

DPF> move ligand_1.pdbqt                    # small molecule
1,4-interactions will be _ignored_ in the non-bonded internal energy
calculation.
/home/anna/bin/autodock4: I'm sorry; I can't find or open "ligand_1.pdbqt"
Real= 0.56,  CPU= 0.52,  System= 0.03

and I have ligand_1.pdbqt in same directory like autodock4.0.  I do not
understand what problem is with this file.

Here is this file:

REMARK  5 active torsions:
REMARK  status: ('A' for Active; 'I' for Inactive)
REMARK    1  A    between atoms: C6_6  and  C7_7
REMARK    2  A    between atoms: C8_8  and  C9_9
REMARK    3  A    between atoms: C10_10  and  C11_11
REMARK    4  A    between atoms: C12_12  and  C13_13
REMARK    5  A    between atoms: C14_14  and  C15_15
ROOT
HETATM    1  C7  REA   500      13.641  29.593  48.398  1.00 46.95     0.009C
HETATM    2  C8  REA   500      14.405  29.204  47.356  1.00 43.72     0.007C
ENDROOT
BRANCH   2   3
HETATM    3  C9  REA   500      14.398  29.470  45.969  1.00 41.91    -0.062C
HETATM    4  C10 REA   500      15.306  28.834  45.186  1.00 42.70     0.007C
HETATM    5  C19 REA   500      13.373  30.415  45.391  1.00 41.86     0.048C
BRANCH   4   6
HETATM    6  C11 REA   500      16.406  27.911  45.516  1.00 41.99     0.001C
HETATM    7  C12 REA   500      17.148  27.268  44.595  1.00 40.11     0.007C
BRANCH   7   8
HETATM    8  C13 REA   500      18.280  26.322  44.917  1.00 35.96    -0.056C
HETATM    9  C14 REA   500      18.760  25.665  43.874  1.00 34.92     0.091C
HETATM   10  C20 REA   500      18.756  26.107  46.348  1.00 40.34     0.048C
BRANCH   9  11
HETATM   11  C15 REA   500      19.734  24.558  43.655  1.00 35.77     0.199C
HETATM   12  O1  REA   500      19.404  23.755  42.704  1.00 29.80    -0.644OA
HETATM   13  O2  REA   500      20.623  24.217  44.564  1.00 26.85    -0.644OA
ENDBRANCH   9  11
ENDBRANCH   7   8
ENDBRANCH   4   6
ENDBRANCH   2   3
BRANCH   1  14
HETATM   14  C6  REA   500      13.815  29.235  49.846  1.00 45.64    -0.048C
HETATM   15  C1  REA   500      14.213  30.479  50.805  1.00 47.12    -0.020C
HETATM   16  C2  REA   500      14.713  29.925  52.198  1.00 48.25     0.014C
HETATM   17  C16 REA   500      15.390  31.390  50.312  1.00 48.48     0.020C
HETATM   18  C17 REA   500      13.017  31.398  51.051  1.00 43.93     0.020C
HETATM   19  C3  REA   500      13.957  28.754  52.825  1.00 44.10     0.005C
HETATM   20  C4  REA   500      13.828  27.597  51.870  1.00 44.95     0.034C
HETATM   21  C5  REA   500      13.594  27.931  50.372  1.00 47.04    -0.077C
HETATM   22  C18 REA   500      13.178  26.627  49.704  1.00 48.16     0.044C
ENDBRANCH   1  14
TORSDOF 5


Thanks a lot for your help.

Anna

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