Hi all,
I am trying to prepare a ligand with antechamber. The job fails and
acdoctor states:
"Warning: There are no hydrogen and halogens in this molecule, it is
highly possible that this molecule has open valence"
The pdb file containing hydrogens (see below) works fine with vmd. I
tried stipping all H atoms and adding them again with pdb4amber, but
that did not work either.
Any suggestions?
ATOM 1 C1 L01 X 900 -10.246 -68.748 -16.541 0.00 0.00
C1 C
ATOM 2 C2 L01 X 900 -9.820 -68.174 -15.341 0.00 0.00
C1 C
ATOM 3 C3 L01 X 900 -9.586 -68.485 -17.745 0.00 0.00
C1 C
ATOM 4 C4 L01 X 900 -8.731 -67.298 -15.283 0.00 0.00
C1 C
ATOM 5 C5 L01 X 900 -8.473 -67.638 -17.715 0.00 0.00
C1 C
ATOM 6 C6 L01 X 900 -8.076 -67.045 -16.490 0.00 0.00
C1 C
ATOM 7 C7 L01 X 900 -6.752 -66.477 -18.180 0.00 0.00
C1 C
ATOM 8 C8 L01 X 900 -3.877 -65.302 -17.176 0.00 0.00
C1 C
ATOM 9 C9 L01 X 900 1.808 -65.798 -14.425 0.00 0.00
C1 C
ATOM 10 C10 L01 X 900 2.033 -63.425 -13.535 0.00 0.00
C1 C
ATOM 11 C11 L01 X 900 3.326 -65.774 -14.672 0.00 0.00
C1 C
ATOM 12 C12 L01 X 900 3.535 -63.525 -13.863 0.00 0.00
C1 C
ATOM 13 C13 L01 X 900 -4.788 -66.894 -19.737 0.00 0.00
C1 C
ATOM 14 C14 L01 X 900 -0.666 -63.091 -16.430 0.00 0.00
C1 C
ATOM 15 C15 L01 X 900 -0.274 -64.309 -14.221 0.00 0.00
C1 C
ATOM 16 C16 L01 X 900 -2.614 -64.266 -15.275 0.00 0.00
C1 C
ATOM 17 C17 L01 X 900 -5.595 -65.843 -18.952 0.00 0.00
C1 C
ATOM 18 C18 L01 X 900 -1.085 -64.283 -15.545 0.00 0.00
C1 C
ATOM 19 N1 L01 X 900 -7.638 -67.267 -18.736 0.00 0.00
C1 N
ATOM 20 N2 L01 X 900 -6.994 -66.277 -16.841 0.00 0.00
C1 N
ATOM 21 N3 L01 X 900 1.256 -64.355 -14.492 0.00 0.00
C1 N
ATOM 22 N4 L01 X 900 -3.476 -64.238 -16.473 0.00 0.00
C1 N
ATOM 23 N5 L01 X 900 -4.732 -64.956 -18.150 0.00 0.00
C1 N
ATOM 24 O1 L01 X 900 -3.568 -66.460 -16.902 0.00 0.00
C1 O
ATOM 25 O2 L01 X 900 3.987 -64.875 -13.779 0.00 0.00
C1 O
ATOM 26 O3 L01 X 900 -0.799 -65.454 -16.270 0.00 0.00
C1 O
ATOM 27 H1 L01 X 900 -11.103 -69.408 -16.540 0.00 0.00
C1 H
ATOM 28 H2 L01 X 900 -10.358 -68.405 -14.431 0.00 0.00
C1 H
ATOM 29 H3 L01 X 900 -9.919 -68.921 -18.675 0.00 0.00
C1 H
ATOM 30 H4 L01 X 900 -8.412 -66.852 -14.352 0.00 0.00
C1 H
ATOM 31 H5 L01 X 900 1.294 -66.400 -15.172 0.00 0.00
C1 H
ATOM 32 H6 L01 X 900 1.575 -66.163 -13.426 0.00 0.00
C1 H
ATOM 33 H7 L01 X 900 1.651 -62.415 -13.684 0.00 0.00
C1 H
ATOM 34 H8 L01 X 900 1.811 -63.762 -12.520 0.00 0.00
C1 H
ATOM 35 H9 L01 X 900 3.536 -65.493 -15.706 0.00 0.00
C1 H
ATOM 36 H10 L01 X 900 3.731 -66.777 -14.531 0.00 0.00
C1 H
ATOM 37 H11 L01 X 900 3.738 -63.126 -14.859 0.00 0.00
C1 H
ATOM 38 H12 L01 X 900 4.109 -62.915 -13.163 0.00 0.00
C1 H
ATOM 39 H13 L01 X 900 -5.417 -67.446 -20.435 0.00 0.00
C1 H
ATOM 40 H14 L01 X 900 -4.328 -67.614 -19.065 0.00 0.00
C1 H
ATOM 41 H15 L01 X 900 -3.982 -66.436 -20.296 0.00 0.00
C1 H
ATOM 42 H16 L01 X 900 -1.266 -63.029 -17.337 0.00 0.00
C1 H
ATOM 43 H17 L01 X 900 0.376 -63.162 -16.744 0.00 0.00
C1 H
ATOM 44 H18 L01 X 900 -0.787 -62.147 -15.901 0.00 0.00
C1 H
ATOM 45 H19 L01 X 900 -0.521 -65.144 -13.564 0.00 0.00
C1 H
ATOM 46 H20 L01 X 900 -0.464 -63.391 -13.661 0.00 0.00
C1 H
ATOM 47 H21 L01 X 900 -2.884 -65.122 -14.651 0.00 0.00
C1 H
ATOM 48 H22 L01 X 900 -2.857 -63.387 -14.677 0.00 0.00
C1 H
ATOM 49 H23 L01 X 900 -6.059 -65.174 -19.678 0.00 0.00
C1 H
ATOM 50 H24 L01 X 900 -6.387 -65.720 -16.262 0.00 0.00
C1 H
ATOM 51 H25 L01 X 900 -3.755 -63.330 -16.808 0.00 0.00
C1 H
ATOM 52 H26 L01 X 900 -4.736 -63.990 -18.449 0.00 0.00
C1 H
ATOM 53 H27 L01 X 900 -1.167 -66.202 -15.770 0.00 0.00
C1 H
ATOM 54 H28 L01 X 900 1.404 -64.011 -15.431 0.00 0.00
C1 H
--
M.Sc. Andreas Tosstorff
Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
Department Pharmazie
LMU München
Butenandtstr. 5-13 ( Haus B)
81377 München
Germany
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Received on Mon Dec 12 2016 - 05:30:03 PST
