[gmx-users] pdb2gmx problems
Ken Rotondi
ksr at chemistry.umass.edu
Tue Jan 17 16:32:48 CET 2006
Hello All,
when I run (using GROMACS3.2.1with a modified .hdb including the RNA
bases)
pdb2gmx -f test.pdb -o test.gro -p test.top -i test.itp -n test.ndx
-ignh
on the attached .pdb file with ff 43a1 (gromos96 official) it converts
successfully. Both the pdb2gmx output:
chain #res #atoms
1 ' ' 4 82
and .top file:
[ molecules ]
; Compound #mols
Protein 1
Indicate that there is one molecule. However, the .pdb file clearly has
a TER statement and a large gap between the second and third
nucleotides. Why does GROMACS think this is one chain? How can I fix
this? If it thinks this is one chain, why doesn't GROMACS issue a long
bond warning between nucleotides 2 and 3?
Also, this is two RNA molecules, the pdb2gmx output correctly states:
"No N- or C-terminus found: this chain appears to contain no protein"
yet the .top states that this is 1 molecule of protein, is this an
issue?
test.pdb:
ATOM 85982 P CYT 2876 21.204 38.244 127.202 1.00 90.16
ATOM 85983 O1P CYT 2876 21.841 36.963 127.601 1.00 90.16
ATOM 85984 O2P CYT 2876 20.444 38.320 125.929 1.00 90.16
ATOM 85985 O5* CYT 2876 20.247 38.715 128.385 1.00 90.16
ATOM 85986 C5* CYT 2876 20.724 38.778 129.727 1.00 90.16
ATOM 85987 C4* CYT 2876 19.688 39.417 130.621 1.00 90.16
ATOM 85988 O4* CYT 2876 19.465 40.787 130.198 1.00 90.16
ATOM 85989 C1* CYT 2876 18.104 41.134 130.400 1.00 90.16
ATOM 85990 N1 CYT 2876 17.522 41.499 129.099 1.00 90.16
ATOM 85991 C6 CYT 2876 18.105 41.096 127.930 1.00 90.16
ATOM 85992 C2 CYT 2876 16.355 42.269 129.076 1.00 90.16
ATOM 85993 O2 CYT 2876 15.849 42.622 130.152 1.00 90.16
ATOM 85994 N3 CYT 2876 15.810 42.610 127.886 1.00 90.16
ATOM 85995 C4 CYT 2876 16.386 42.210 126.750 1.00 90.16
ATOM 85996 N4 CYT 2876 15.813 42.568 125.598 1.00 90.16
ATOM 85997 C5 CYT 2876 17.576 41.425 126.744 1.00 90.16
ATOM 85998 C2* CYT 2876 17.418 39.931 131.050 1.00 90.16
ATOM 85999 O2* CYT 2876 17.420 40.082 132.456 1.00 90.16
ATOM 86000 C3* CYT 2876 18.306 38.786 130.579 1.00 90.16
ATOM 86001 O3* CYT 2876 18.230 37.667 131.455 1.00 90.16
ATOM 86002 P ADE 2877 17.220 36.462 131.121 1.00 85.57
ATOM 86003 O1P ADE 2877 17.365 35.450 132.197 1.00 85.57
ATOM 86004 O2P ADE 2877 17.422 36.062 129.705 1.00 85.57
ATOM 86005 O5* ADE 2877 15.777 37.124 131.252 1.00 85.57
ATOM 86006 C5* ADE 2877 15.322 37.645 132.498 1.00 85.57
ATOM 86007 C4* ADE 2877 13.982 38.318 132.324 1.00 85.57
ATOM 86008 O4* ADE 2877 14.119 39.444 131.417 1.00 85.57
ATOM 86009 C1* ADE 2877 12.927 39.594 130.661 1.00 85.57
ATOM 86010 N9 ADE 2877 13.264 39.467 129.244 1.00 85.57
ATOM 86011 C4 ADE 2877 12.493 39.880 128.185 1.00 85.57
ATOM 86012 N3 ADE 2877 11.289 40.477 128.235 1.00 85.57
ATOM 86013 C2 ADE 2877 10.841 40.734 127.008 1.00 85.57
ATOM 86014 N1 ADE 2877 11.415 40.481 125.826 1.00 85.57
ATOM 86015 C6 ADE 2877 12.625 39.880 125.810 1.00 85.57
ATOM 86016 N6 ADE 2877 13.198 39.627 124.631 1.00 85.57
ATOM 86017 C5 ADE 2877 13.209 39.555 127.047 1.00 85.57
ATOM 86018 N7 ADE 2877 14.412 38.949 127.381 1.00 85.57
ATOM 86019 C8 ADE 2877 14.396 38.920 128.692 1.00 85.57
ATOM 86020 C2* ADE 2877 11.945 38.523 131.144 1.00 85.57
ATOM 86021 O2* ADE 2877 11.111 39.066 132.147 1.00 85.57
ATOM 86022 C3* ADE 2877 12.900 37.467 131.682 1.00 85.57
ATOM 86023 O3* ADE 2877 12.315 36.513 132.574 1.00 85.57
TER
ATOM 86024 P CYT 4 81.895 101.701 7.632 1.00 94.72
ATOM 86025 O2P CYT 4 83.321 101.006 7.355 1.00 94.72
ATOM 86026 O1P CYT 4 81.655 102.878 6.560 1.00 94.72
ATOM 86027 O5* CYT 4 81.147 100.998 7.544 1.00 94.72
ATOM 86028 C5* CYT 4 81.639 99.722 7.962 1.00 94.72
ATOM 86029 C4* CYT 4 83.139 99.613 7.817 1.00 94.72
ATOM 86030 O4* CYT 4 83.507 99.864 6.435 1.00 94.72
ATOM 86031 C1* CYT 4 84.739 100.566 6.388 1.00 94.72
ATOM 86032 N1 CYT 4 84.503 101.863 5.735 1.00 94.72
ATOM 86033 C6 CYT 4 83.234 102.347 5.581 1.00 94.72
ATOM 86034 C2 CYT 4 85.600 102.598 5.271 1.00 94.72
ATOM 86035 O2 CYT 4 86.741 102.136 5.425 1.00 94.72
ATOM 86036 N3 CYT 4 85.389 103.791 4.668 1.00 94.72
ATOM 86037 C4 CYT 4 84.145 104.253 4.522 1.00 94.72
ATOM 86038 N4 CYT 4 83.983 105.434 3.920 1.00 94.72
ATOM 86039 C5 CYT 4 83.011 103.526 4.986 1.00 94.72
ATOM 86040 C2* CYT 4 85.248 100.691 7.826 1.00 94.72
ATOM 86041 O2* CYT 4 86.116 99.615 8.121 1.00 94.72
ATOM 86042 C3* CYT 4 83.945 100.627 8.613 1.00 94.72
ATOM 86043 O3* CYT 4 84.157 100.174 9.946 1.00 94.72
ATOM 86044 P CYT 5 84.453 101.240 11.112 1.00 93.36
ATOM 86045 O1P CYT 5 84.493 100.492 12.394 1.00 93.36
ATOM 86046 O2P CYT 5 83.513 102.379 10.955 1.00 93.36
ATOM 86047 O5* CYT 5 85.925 101.760 10.795 1.00 93.36
ATOM 86048 C5* CYT 5 87.050 100.894 10.922 1.00 93.36
ATOM 86049 C4* CYT 5 88.317 101.623 10.538 1.00 93.36
ATOM 86050 O4* CYT 5 88.250 101.994 9.136 1.00 93.36
ATOM 86051 C1* CYT 5 88.868 103.256 8.945 1.00 93.36
ATOM 86052 N1 CYT 5 87.851 104.195 8.448 1.00 93.36
ATOM 86053 C6 CYT 5 86.519 103.894 8.527 1.00 93.36
ATOM 86054 C2 CYT 5 88.268 105.407 7.892 1.00 93.36
ATOM 86055 O2 CYT 5 89.483 105.652 7.833 1.00 93.36
ATOM 86056 N3 CYT 5 87.341 106.278 7.433 1.00 93.36
ATOM 86057 C4 CYT 5 86.043 105.976 7.515 1.00 93.36
ATOM 86058 N4 CYT 5 85.162 106.865 7.050 1.00 93.36
ATOM 86059 C5 CYT 5 85.590 104.747 8.077 1.00 93.36
ATOM 86060 C2* CYT 5 89.465 103.677 10.289 1.00 93.36
ATOM 86061 O2* CYT 5 90.812 103.258 10.366 1.00 93.36
ATOM 86062 C3* CYT 5 88.560 102.937 11.264 1.00 93.36
ATOM 86063 O3* CYT 5 89.201 102.720 12.516 1.00 93.36
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