VMD-L Mailing List

From: Marc Charendoff (mcharend_at_sbcglobal.net)
Date: Wed Aug 10 2011 - 23:10:27 CDT

Hello,

    I am trying to create the hydrolysis product of a lactone ring in
Molefacture from an existing structure so as to show the resulting alcohol and
carboxylate functional groups. Everything looks ok in Molefacture, but when I
write the resulting pdb file and reopen it in VMD I still see that the old
carbonyl carbon to ether oxygen linkage remains. What am I missing? Any guidance
anyone could provide would be greatly appreciated. My current (failed structure)
is below:

REMARK original generated coordinate pdb file
HETATM 1 OAO UNK B 253 29.310 34.583 39.046 1.00 0.00 MOL O
HETATM 2 CAN UNK B 253 28.739 33.746 38.365 1.00 0.00 MOL C
HETATM 3 OAR UNK B 253 28.383 33.934 37.053 1.00 0.00 MOL O
HETATM 4 CAP UNK B 253 29.367 32.494 36.772 1.00 0.00 MOL C
HETATM 5 CAQ UNK B 253 28.673 31.448 37.720 1.00 0.00 MOL C
HETATM 6 CAM UNK B 253 28.249 32.381 38.825 1.00 0.00 MOL C
HETATM 7 NAK UNK B 253 27.290 32.448 39.923 1.00 0.00 MOL N
HETATM 8 HA2 UNK B 253 26.388 32.836 39.732 1.00 0.00 MOL H
HETATM 9 CAJ UNK B 253 27.531 32.036 41.135 1.00 0.00 MOL C
HETATM 10 OAL UNK B 253 28.345 31.134 41.344 1.00 0.00 MOL O
HETATM 11 CAI UNK B 253 26.766 32.648 42.312 1.00 0.00 MOL C
HETATM 12 CAH UNK B 253 25.626 33.644 42.084 1.00 0.00 MOL C
HETATM 13 CAG UNK B 253 25.773 35.117 41.669 1.00 0.00 MOL C
HETATM 14 CAF UNK B 253 24.963 36.102 42.502 1.00 0.00 MOL C
HETATM 15 CAE UNK B 253 25.869 36.510 43.652 1.00 0.00 MOL C
HETATM 16 CAD UNK B 253 25.128 37.706 44.254 1.00 0.00 MOL C
HETATM 17 CAC UNK B 253 24.353 37.255 45.496 1.00 0.00 MOL C
HETATM 18 CAB UNK B 253 25.083 36.081 46.154 1.00 0.00 MOL C
HETATM 19 CAA UNK B 253 24.070 35.189 46.874 1.00 0.00 MOL C
HETATM 20 CAS UNK B 253 23.084 34.560 45.886 1.00 0.00 MOL C
HETATM 21 CAT UNK B 253 23.849 33.685 44.890 1.00 0.00 MOL C
HETATM 22 OAM UNK B 253 29.738 32.082 35.940 1.00 0.00 MOL O
END

The desired product (w/regards to the opened lactone ring) is as follows:

HETATM 2104 O4 C6L A 253 -15.207 -7.751 15.430 0.90 20.62 O
HETATM 2105 C5 C6L A 253 -16.064 -6.960 15.205 0.90 21.63 C
HETATM 2106 C6 C6L A 253 -16.833 -6.344 16.384 0.90 24.08 C
HETATM 2107 C7 C6L A 253 -17.971 -5.350 16.157 0.90 29.16 C
HETATM 2108 C8 C6L A 253 -17.824 -3.877 15.742 0.90 31.82 C
HETATM 2109 C9 C6L A 253 -18.634 -2.892 16.575 0.90 30.57 C
HETATM 2110 C10 C6L A 253 -17.724 -2.483 17.730 0.90 30.72 C
HETATM 2111 N1 C6L A 253 -16.307 -6.546 13.996 0.90 21.59 N
HETATM 2112 C3 C6L A 253 -15.573 -6.989 12.814 0.90 21.15 C
HETATM 2113 C4 C6L A 253 -14.550 -5.958 12.306 0.90 21.16 C
HETATM 2114 O2 C6L A 253 -14.258 -5.884 11.135 0.90 19.59 O
HETATM 2115 O1 C6L A 253 -13.945 -5.227 13.080 0.90 17.44 O
HETATM 2116 C2 C6L A 253 -16.571 -7.274 11.693 0.90 22.47 C
HETATM 2117 C1 C6L A 253 -16.106 -8.309 10.659 0.90 22.14 C
HETATM 2118 O3 C6L A 253 -15.111 -7.792 9.768 0.90 20.66 O
END