AMBER Archive (2005)

Subject: AMBER: problems with "protonate"

From: Kenley Barrett (kenley.barrett_at_gmail.com)
Date: Thu Apr 07 2005 - 21:27:07 CDT

I am having some difficulties with the protonate command. I have an
"abnormal" residue in my protein: a methylated histidine. For some
reason with this residue (and not with any of the normal residues) the
protonate command leads to the placement of atoms that are named with
a "?" I don't know whether I should assume that "?" refers to a
hydrogen or whether I should be concerned about this error. The atom
entries from the pdb file, before and after running protonate, are cut
and pasted below. I would very much appreciate any advice that anyone
has.

Thanks,
Kenley

before protonate:
HETATM 526 N HIC A 73 36.576 54.962 57.432 1.00 20.71
HETATM 527 CA HIC A 73 36.905 55.235 58.813 1.00 21.45
HETATM 528 C HIC A 73 36.440 56.637 59.173 1.00 22.93
HETATM 529 O HIC A 73 37.023 57.318 60.017 1.00 24.12
HETATM 530 CB HIC A 73 38.391 55.124 59.068 1.00 22.40
HETATM 531 CG HIC A 73 38.811 53.664 58.958 1.00 27.20
HETATM 532 ND1 HIC A 73 38.271 52.576 59.534 1.00 27.57
HETATM 533 CD2 HIC A 73 39.822 53.216 58.134 1.00 27.07
HETATM 534 CE1 HIC A 73 38.895 51.516 59.085 1.00 28.32
HETATM 535 NE2 HIC A 73 39.836 51.904 58.245 1.00 28.62
HETATM 536 CZ HIC A 73 40.825 51.000 57.582 1.00 28.06

after protonate:
HETATM 1042 N HIC A 73 36.576 54.962 57.432
HETATM 1043 H HIC A 73 36.036 54.135 57.221
HETATM 1044 CA HIC A 73 36.905 55.235 58.813
HETATM 1045 HA HIC A 73 36.394 54.531 59.436
HETATM 1046 C HIC A 73 36.440 56.637 59.173
HETATM 1047 O HIC A 73 37.023 57.318 60.017
HETATM 1048 CB HIC A 73 38.391 55.124 59.068
HETATM 1049 3HB HIC A 73 38.614 55.488 60.052
HETATM 1050 2HB HIC A 73 38.924 55.706 58.342
HETATM 1051 CG HIC A 73 38.811 53.664 58.958
HETATM 1052 ND1 HIC A 73 38.271 52.576 59.534
HETATM 1053 CD2 HIC A 73 39.822 53.216 58.134
HETATM 1054 ? HIC A 73 40.475 53.823 57.518
HETATM 1055 CE1 HIC A 73 38.895 51.516 59.085
HETATM 1056 ? HIC A 73 38.675 50.490 59.358
HETATM 1057 NE2 HIC A 73 39.836 51.904 58.245
HETATM 1058 ? HIC A 73 40.472 51.287 57.760
HETATM 1059 CZ HIC A 73 40.825 51.000 57.582
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