[gmx-users] A query
Anik Sen
aniksen at csmcri.org
Tue Jan 31 11:04:55 CET 2012
Hello,
Am anik. Am using gromacs 4.5.5
I could not find the proper reason of the foillowig failure of my job. please help.
The following is a part of the dna pdb file, which I am using:
ATOM 1 O5' DG5 X 1 13.663 36.760 21.465 0.00 0.00
ATOM 2 C1' DG5 X 1 14.791 36.040 21.150 0.00 0.00
ATOM 3 C4' DG5 X 1 14.771 34.703 21.873 0.00 0.00
ATOM 4 O4' DG5 X 1 16.017 34.553 22.577 0.00 0.00
ATOM 5 C5' DG5 X 1 13.724 34.528 22.970 0.00 0.00
ATOM 6 O3' DG5 X 1 13.540 33.118 23.234 0.00 0.00
ATOM 7 C3' DG5 X 1 14.362 35.323 24.108 0.00 0.00
ATOM 8 C2' DG5 X 1 15.856 35.044 23.903 0.00 0.00
ATOM 9 N1 DG5 X 1 16.753 36.193 24.040 0.00 0.00
ATOM 10 C8 DG5 X 1 16.484 37.562 24.004 0.00 0.00
ATOM 11 N7 DG5 X 1 17.551 38.308 24.156 0.00 0.00
ATOM 12 C4 DG5 X 1 18.589 37.359 24.268 0.00 0.00
ATOM 13 C6 DG5 X 1 19.989 37.514 24.448 0.00 0.00
ATOM 14 O6 DG5 X 1 20.648 38.553 24.534 0.00 0.00
ATOM 15 N9 DG5 X 1 20.645 36.287 24.525 0.00 0.00
ATOM 16 C2 DG5 X 1 20.048 35.045 24.439 0.00 0.00
ATOM 17 N3 DG5 X 1 20.848 33.965 24.540 0.00 0.00
ATOM 18 N5 DG5 X 1 18.753 34.884 24.262 0.00 0.00
ATOM 19 C5 DG5 X 1 18.095 36.074 24.193 0.00 0.00
ATOM 20 P DT X 2 12.650 32.528 24.445 0.00 0.00
ATOM 21 O1P DT X 2 12.016 31.284 23.943 0.00 0.00
ATOM 22 O2P DT X 2 11.806 33.610 25.015 0.00 0.00
ATOM 23 O5' DT X 2 13.743 32.102 25.531 0.00 0.00
ATOM 24 C3' DT X 2 14.653 31.088 25.184 0.00 0.00
ATOM 25 C2' DT X 2 15.813 31.114 26.126 0.00 0.00
ATOM 26 O3' DT X 2 16.429 32.408 26.092 0.00 0.00
ATOM 27 C5' DT X 2 15.420 30.906 27.570 0.00 0.00
ATOM 28 O4' DT X 2 15.818 29.609 27.955 0.00 0.00
ATOM 29 C4' DT X 2 16.171 31.996 28.340 0.00 0.00
ATOM 30 C1' DT X 2 17.115 32.536 27.293 0.00 0.00
ATOM 31 N3 DT X 2 17.425 33.937 27.428 0.00 0.00
ATOM 32 C2 DT X 2 18.741 34.313 27.581 0.00 0.00
ATOM 33 O2 DT X 2 19.667 33.515 27.649 0.00 0.00
ATOM 34 N1 DT X 2 18.932 35.671 27.666 0.00 0.00
But my job is failing, as shown below:
[ganguly at localhost anik]$ pdb2gmx -f dna-A.pdb -o dna-B.pdb -p topol.top
:-) G R O M A C S (-:
GROtesk MACabre and Sinister
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
...................................................................................
...................................................................................
...................................................................................
Opening force field file /usr/local/gromacs/share/gromacs/top/amber03.ff/dna.arn
Opening force field file /usr/local/gromacs/share/gromacs/top/amber03.ff/rna.arn
Checking for duplicate atoms....
Now there are 657 atoms. Deleted 7 duplicates.
-------------------------------------------------------
Program pdb2gmx, VERSION 4.5.5
Source code file: pgutil.c, line: 91
Fatal error:
Atom N3 is used in an interaction of type atom in the topology
database, but an atom of that name was not found in residue
number 31.
========================================================
Anik Sen
Student
CSIR-Central Salt & Marine Chemicals Research Institute,
Gijubhai Badheka Marg.
Bhavnagar, Gujarat 364002
[www.csmcri.org]
========================================================
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