[gmx-users] pdb2gmx fails because of imaginary "Residue E"
kolnkempff
kolnkempff at gmail.com
Sat Nov 30 01:24:15 CET 2013
pdb2gmx produces error message:
Fatal error:
Residue 'E' not found in residue topology database
But there is no "Residue 'E' " in my pdb file (see below). I have verified
that all residues in the pdb file are listed in ffamber03.rtp and pdb2gmx
does identify the ACE and NME caps.
COMPND UNNAMED
AUTHOR GENERATED BY OPEN BABEL 2.3.1
ATOM 1 N PHE 2 0.720 0.859 -0.499 1.00 0.00 N
ATOM 2 C PHE 2 0.760 -0.439 0.174 1.00 0.00 C
ATOM 3 C PHE 2 2.125 -1.161 0.111 1.00 0.00 C
ATOM 4 O PHE 2 2.253 -2.263 0.634 1.00 0.00 O
ATOM 5 H PHE 2 0.176 0.905 -1.352 1.00 0.00 H
ATOM 6 H PHE 2 0.585 -0.253 1.240 1.00 0.00 H
ATOM 7 C PHE 2 -0.336 -1.383 -0.373 1.00 0.00 C
ATOM 8 C PHE 2 -1.743 -0.858 -0.186 1.00 0.00 C
ATOM 9 H PHE 2 -0.200 -2.340 0.138 1.00 0.00 H
ATOM 10 H PHE 2 -0.145 -1.567 -1.440 1.00 0.00 H
ATOM 11 C PHE 2 -4.354 0.139 0.179 1.00 0.00 C
ATOM 12 C PHE 2 -2.316 -0.794 1.094 1.00 0.00 C
ATOM 13 C PHE 2 -2.504 -0.416 -1.277 1.00 0.00 C
ATOM 14 C PHE 2 -3.799 0.078 -1.100 1.00 0.00 C
ATOM 15 C PHE 2 -3.607 -0.301 1.276 1.00 0.00 C
ATOM 16 H PHE 2 -1.744 -1.138 1.954 1.00 0.00 H
ATOM 17 H PHE 2 -2.086 -0.476 -2.281 1.00 0.00 H
ATOM 18 H PHE 2 -4.373 0.412 -1.961 1.00 0.00 H
ATOM 19 H PHE 2 -4.033 -0.263 2.276 1.00 0.00 H
ATOM 20 H PHE 2 -5.362 0.519 0.320 1.00 0.00 H
HETATM 21 C ACE 1 0.873 2.036 0.208 1.00 0.00
C
HETATM 22 O ACE 1 1.301 2.055 1.353 1.00 0.00
O
HETATM 23 C ACE 1 0.484 3.302 -0.540 1.00 0.00
C
HETATM 24 H ACE 1 1.253 4.060 -0.375 1.00 0.00
H
HETATM 25 H ACE 1 -0.451 3.685 -0.116 1.00 0.00
H
HETATM 26 H ACE 1 0.345 3.153 -1.616 1.00 0.00
H
HETATM 27 N NME 3 3.115 -0.507 -0.549 1.00 0.00
N
HETATM 28 C NME 3 4.474 -1.010 -0.616 1.00 0.00
C
HETATM 29 H NME 3 5.163 -0.381 -0.040 1.00 0.00
H
HETATM 30 H NME 3 4.474 -2.015 -0.195 1.00 0.00
H
HETATM 31 H NME 3 4.822 -1.054 -1.654 1.00 0.00
H
HETATM 32 H NME 3 2.906 0.422 -0.885 1.00 0.00
H
END
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