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On 1/02/2012 4:19 PM, Anik Sen wrote:
<blockquote
cite="mid:BDE9D87D31C781498280133FD1BE69A51DD2A379@EXCHANGE.csmcri.org"
type="cite">
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<div style="direction: ltr; font-family: Tahoma; color: rgb(0, 0,
0); font-size: 10pt;">Hello,<br>
<span style="background-color: white;"><font
color="black" face="Tahoma" size="2"><span dir="ltr"
style="font-size: 10pt;">Am anik. Am using gromacs 4.5.5<br>
<br>
But the dna.rtp file contains the atom bname N3 under the
residue file DT. So whats the problem then.<br>
</span></font></span></div>
</blockquote>
<br>
Yes, that's the reason from the problem. Your input structure
doesn't have that... I said:<br>
<br>
<blockquote type="cite">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.</blockquote>
<br>
*Your input structure* doesn't match the .rtp. You need to change
the atom/residue naming of your input structure to conform.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:BDE9D87D31C781498280133FD1BE69A51DD2A379@EXCHANGE.csmcri.org"
type="cite">
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<br>
the dna.rtp file for DT<br>
[ DT ]<br>
[ atoms ]<br>
P P 1.16590 1<br>
O2 O1P -0.77610 2<br>
O2 O2P -0.77610 3<br>
OS O5' -0.49540 4<br>
CT C5' -0.00690 5<br>
H1 H5'1 0.07540 6<br>
H1 H5'2 0.07540 7<br>
CT C4' 0.16290 8<br>
H1 H4' 0.11760 9<br>
OS O4' -0.36910 10<br>
CT C1' 0.06800 11<br>
H2 H1' 0.18040 12<br>
N* N1 -0.02390 13<br>
CM C6 -0.22090 14<br>
H4 H6 0.26070 15<br>
CM C5 0.00250 16<br>
CT C7 -0.22690 17<br>
HC H71 0.07700 18<br>
HC H72 0.07700 19<br>
HC H73 0.07700 20<br>
C C4 0.51940 21<br>
O O4 -0.55630 22<br>
NA N3 -0.43400 23<br>
H H3 0.34200 24<br>
C C2 0.56770 25<br>
O O2 -0.58810 26<br>
CT C3' 0.07130 27<br>
H1 H3' 0.09850 28<br>
CT C2' -0.08540 29<br>
HC H2'1 0.07180 30<br>
HC H2'2 0.07180 31<br>
OS O3' -0.52320 32<br>
<br>
</span></font></span>
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font-size: 16px;">
<hr tabindex="-1">
<div style="direction: ltr;" id="divRpF311551"><font
color="#000000" face="Tahoma" size="2"><b>From:</b>
<a class="moz-txt-link-abbreviated" href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a>
[<a class="moz-txt-link-abbreviated" href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a>] on behalf of Mark Abraham
[<a class="moz-txt-link-abbreviated" href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>]<br>
<b>Sent:</b> Tuesday, January 31, 2012 7:09 PM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> Re: [gmx-users] A query<br>
</font><br>
</div>
<div>On 31/01/2012 9:04 PM, Anik Sen wrote:
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Hello,<br>
<span style="background-color: white;"><font
color="black" face="Tahoma" size="2"><span dir="ltr"
style="font-size: 10pt;">Am anik. Am using gromacs
4.5.5<br>
I could not find the proper reason of the
foillowig failure of my job. please help.<br>
<br>
</span></font></span><span style="background-color:
white;"><font color="black" face="Tahoma" size="2"><span
dir="ltr" style="font-size: 10pt;"><b>The
following is a part of the dna pdb file, which I
am using:<br>
<br>
</b>ATOM 1 O5' DG5 X 1 13.663
36.760 21.465 0.00 0.00
<br>
ATOM 2 C1' DG5 X 1 14.791 36.040
21.150 0.00 0.00 <br>
ATOM 3 C4' DG5 X 1 14.771 34.703
21.873 0.00 0.00 <br>
ATOM 4 O4' DG5 X 1 16.017 34.553
22.577 0.00 0.00 <br>
ATOM 5 C5' DG5 X 1 13.724 34.528
22.970 0.00 0.00 <br>
ATOM 6 O3' DG5 X 1 13.540 33.118
23.234 0.00 0.00 <br>
ATOM 7 C3' DG5 X 1 14.362 35.323
24.108 0.00 0.00 <br>
ATOM 8 C2' DG5 X 1 15.856 35.044
23.903 0.00 0.00 <br>
ATOM 9 N1 DG5 X 1 16.753 36.193
24.040 0.00 0.00 <br>
ATOM 10 C8 DG5 X 1 16.484 37.562
24.004 0.00 0.00 <br>
ATOM 11 N7 DG5 X 1 17.551 38.308
24.156 0.00 0.00 <br>
ATOM 12 C4 DG5 X 1 18.589 37.359
24.268 0.00 0.00 <br>
ATOM 13 C6 DG5 X 1 19.989 37.514
24.448 0.00 0.00 <br>
ATOM 14 O6 DG5 X 1 20.648 38.553
24.534 0.00 0.00 <br>
ATOM 15 N9 DG5 X 1 20.645 36.287
24.525 0.00 0.00 <br>
ATOM 16 C2 DG5 X 1 20.048 35.045
24.439 0.00 0.00 <br>
ATOM 17 N3 DG5 X 1 20.848 33.965
24.540 0.00 0.00 <br>
ATOM 18 N5 DG5 X 1 18.753 34.884
24.262 0.00 0.00 <br>
ATOM 19 C5 DG5 X 1 18.095 36.074
24.193 0.00 0.00 <br>
ATOM 20 P DT X 2 12.650 32.528
24.445 0.00 0.00 <br>
ATOM 21 O1P DT X 2 12.016 31.284
23.943 0.00 0.00 <br>
ATOM 22 O2P DT X 2 11.806 33.610
25.015 0.00 0.00 <br>
ATOM 23 O5' DT X 2 13.743 32.102
25.531 0.00 0.00 <br>
ATOM 24 C3' DT X 2 14.653 31.088
25.184 0.00 0.00 <br>
ATOM 25 C2' DT X 2 15.813 31.114
26.126 0.00 0.00 <br>
ATOM 26 O3' DT X 2 16.429 32.408
26.092 0.00 0.00 <br>
ATOM 27 C5' DT X 2 15.420 30.906
27.570 0.00 0.00 <br>
ATOM 28 O4' DT X 2 15.818 29.609
27.955 0.00 0.00 <br>
ATOM 29 C4' DT X 2 16.171 31.996
28.340 0.00 0.00 <br>
ATOM 30 C1' DT X 2 17.115 32.536
27.293 0.00 0.00 <br>
ATOM 31 N3 DT X 2 17.425 33.937
27.428 0.00 0.00 <br>
ATOM 32 C2 DT X 2 18.741 34.313
27.581 0.00 0.00 <br>
ATOM 33 O2 DT X 2 19.667 33.515
27.649 0.00 0.00 <br>
ATOM 34 N1 DT X 2 18.932 35.671
27.666 0.00 0.00 <b><br>
<br>
<br>
But my job is failing, as shown below:<br>
<br>
<br>
</b>[ganguly@localhost anik]$ pdb2gmx -f dna-A.pdb
-o dna-B.pdb -p topol.top<br>
:-) G R O M A C S
(-:<br>
<br>
GROtesk MACabre and
Sinister<br>
<br>
:-) VERSION 4.5.5
(-:<br>
<br>
Written by Emile Apol, Rossen Apostolov,
Herman J.C. Berendsen,<br>
Aldert van Buuren, Pär Bjelkmar, Rudi van
Drunen, Anton Feenstra, <br>
Gerrit Groenhof, Peter Kasson, Per
Larsson, Pieter Meulenhoff, <br>
Teemu Murtola, Szilard Pall, Sander
Pronk, Roland Schulz, <br>
Michael Shirts, Alfons Sijbers,
Peter Tieleman,<br>
<br>
...................................................................................<br>
...................................................................................<br>
...................................................................................<br>
<br>
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber03.ff/dna.arn<br>
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber03.ff/rna.arn<br>
Checking for duplicate atoms....<br>
Now there are 657 atoms. Deleted 7 duplicates.<br>
<br>
-------------------------------------------------------<br>
Program pdb2gmx, VERSION 4.5.5<br>
Source code file: pgutil.c, line: 91<br>
<br>
Fatal error:<br>
Atom N3 is used in an interaction of type atom in
the topology<br>
database, but an atom of that name was not found
in residue<br>
number 31 </span></font></span></div>
</blockquote>
<br>
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.<br>
<br>
Mark<br>
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