[gmx-users] A query
Anik Sen
aniksen at csmcri.org
Wed Feb 1 06:19:08 CET 2012
Hello,
Am anik. Am using gromacs 4.5.5
But the dna.rtp file contains the atom bname N3 under the residue file DT. So whats the problem then.
the dna.rtp file for DT
[ DT ]
[ atoms ]
P P 1.16590 1
O2 O1P -0.77610 2
O2 O2P -0.77610 3
OS O5' -0.49540 4
CT C5' -0.00690 5
H1 H5'1 0.07540 6
H1 H5'2 0.07540 7
CT C4' 0.16290 8
H1 H4' 0.11760 9
OS O4' -0.36910 10
CT C1' 0.06800 11
H2 H1' 0.18040 12
N* N1 -0.02390 13
CM C6 -0.22090 14
H4 H6 0.26070 15
CM C5 0.00250 16
CT C7 -0.22690 17
HC H71 0.07700 18
HC H72 0.07700 19
HC H73 0.07700 20
C C4 0.51940 21
O O4 -0.55630 22
NA N3 -0.43400 23
H H3 0.34200 24
C C2 0.56770 25
O O2 -0.58810 26
CT C3' 0.07130 27
H1 H3' 0.09850 28
CT C2' -0.08540 29
HC H2'1 0.07180 30
HC H2'2 0.07180 31
OS O3' -0.52320 32
________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Mark Abraham [Mark.Abraham at anu.edu.au]
Sent: Tuesday, January 31, 2012 7:09 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] A query
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
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