[gmx-users] pdb2gmx problems

Tue Jan 17 19:34:26 CET 2006

Ken Rotondi wrote:
> 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?

You need to add different chain labels, otherwise gromacs stitches it 
all together into one "protein"
>
> 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?
Yes, run with -inter and select No termini
>
>
> 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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>
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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