[gmx-users] A query
Mark Abraham
Mark.Abraham at anu.edu.au
Tue Jan 31 14:39:13 CET 2012
On 31/01/2012 9:04 PM, Anik Sen wrote:
> 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
pdb2gmx can only match atom and residue names it finds in the topology
database (.rtp). Your input structure lacks a (correctly named) N3 atom
in residue 31, which I think pdb2gmx looked for when building hydrogen
atoms.
Mark
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120201/81f7247a/attachment.html>
More information about the gromacs.org_gmx-users
mailing list