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<DIV><FONT face=Arial color=#0000ff size=2><SPAN class=166121413-02112006>See
the following from the archive for a possible source of the "number of
coordinates...does not match" error.</SPAN></FONT></DIV>
<DIV><FONT face=Arial color=#0000ff size=2></FONT> </DIV>
<DIV><FONT face=Arial color=#0000ff size=2><A
href="http://www.gromacs.org/pipermail/gmx-users/2006-October/024223.html">http://www.gromacs.org/pipermail/gmx-users/2006-October/024223.html</A></FONT></DIV>
<DIV> </DIV>
<DIV> </DIV><!-- Converted from text/rtf format -->
<P><SPAN lang=en-us><FONT face=Arial color=#000000 size=2>Thanks,</FONT></SPAN>
<BR><SPAN lang=en-us><FONT face="Brush Script MT" color=#0000ff
size=6>Jonathan</FONT></SPAN> </P>
<P><SPAN lang=en-us><FONT face=Arial color=#ff0000
size=2>____________________________</FONT></SPAN> <BR><SPAN lang=en-us><B><FONT
face="Comic Sans MS" color=#808080 size=2>Jonathan Moore,
Ph.D.</FONT></B></SPAN> <BR><SPAN lang=en-us><FONT face=Arial color=#808080
size=1>Research and Engineering Sciences - New Products</FONT></SPAN> <BR><SPAN
lang=en-us><FONT face=Arial color=#808080 size=1>Core R&D</FONT></SPAN>
<BR><SPAN lang=en-us><FONT face=Arial color=#808080 size=1>The Dow Chemical
Company</FONT></SPAN> <BR><SPAN lang=en-us><FONT face=Arial color=#808080
size=1>1702 Building, Office 300E</FONT></SPAN> <BR><SPAN lang=en-us><FONT
face=Arial color=#808080 size=1>Midland, MI 48674 USA</FONT></SPAN>
<BR><SPAN lang=en-us><FONT face=Arial color=#808080 size=1>Phone: (989)
636-9765 </FONT></SPAN><BR><SPAN lang=en-us><FONT face=Arial color=#808080
size=1>Fax: (989) 636-4019</FONT></SPAN> <BR><SPAN lang=en-us><FONT face=Arial
color=#808080 size=1>E Mail: jmoore2@dow.com</FONT></SPAN> </P>
<BLOCKQUOTE dir=ltr style="MARGIN-RIGHT: 0px">
<DIV></DIV>
<DIV class=OutlookMessageHeader lang=en-us dir=ltr align=left><FONT
face=Tahoma size=2>-----Original Message-----<BR><B>From:</B>
gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <B>On
Behalf Of </B>Xiangyang Liu<BR><B>Sent:</B> Thursday, November 02, 2006 6:32
AM<BR><B>To:</B> Discussion list for GROMACS users<BR><B>Subject:</B> Re:
[gmx-users] about the topology file<BR><BR></FONT></DIV>
<DIV>hello Tsjerk:</DIV>
<DIV>Thank you very much! That does work, but another problem appeared as
following:</DIV>
<DIV>creating statusfile for 1 node...<BR>checking input for internal
consistency...<BR>calling /lib/cpp...<BR>processing topology...<BR>Generated
1284 of the 1485 non-bonded parameter combinations<BR>WARNING 1 [file "
com.top", line 519]:<BR> Too few parameters on line (source file
toppush.c, line 932)<BR>WARNING 2 [file "com.top", line 520]:<BR> Too
few parameters on line (source file toppush.c, line 932)<BR>processing
coordinates... <BR>Fatal error: number of coordinates in coordinate file
(com_wat.gro,
2837)<BR>
does not match topology (com.top, 0)<BR>actually i only perform the
following:</DIV>
<DIV>
<P class=MsoNormal style="MARGIN: 0pt"><SPAN lang=EN-US><FONT
face="Times New Roman">editconf –bt cubic –f com.gro –o com_box.gro –d
0.8</FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0pt"><SPAN lang=EN-US><FONT
face="Times New Roman">genbox –cp com_box.gro –cs spc216.gro –p com.top
–o com_wat.gro</FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0pt"><SPAN lang=EN-US><FONT
face="Times New Roman">grompp –f em.mdp –c com_wat.gro –p com.top –o
com_em.tpr</FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0pt"><SPAN lang=EN-US><FONT
face="Times New Roman">and my com.gro file was as following:</FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0pt"><SPAN lang=EN-US>PRODRG
COORDS<BR> 80<BR> 1DRG
CAH 1 -0.832 -0.624
-0.960<BR> 1DRG CAS
2 -0.746 -0.538 -0.867<BR> 1DRG
CAT 3 -0.710 -0.410 -
0.942<BR> 1DRG CBI
4 -0.621 -0.618 -0.830<BR> 1DRG
CCF 5 -0.555 -0.585
-0.694<BR> 1DRG CCG
6 -0.647 -0.615 -0.575<BR> 1DRG
OCU 7 -0.750 -0.706
-0.587<BR> 1DRG OBJ
8 - 0.629 -0.560 -0.467<BR> 1DRG
NCE 9 -0.506 -0.445
-0.688<BR> 1DRG HAG 10
-0.556 -0.385 -0.626<BR> 1DRG
CCD 11 -0.401 -0.405
-0.761<BR> 1DRG OBH 12
-0.345 -0.480 -0.843<BR> 1DRG
CCC 13 - 0.347 -0.263
-0.745<BR> 1DRG CBG 14
-0.439 -0.163 -0.817<BR> 1DRG
CAQ 15 -0.381 -0.024
-0.851<BR> 1DRG CAG 16
-0.248 -0.030 -0.926<BR> 1DRG
CAR 17 -0.363 0.065
-0.727<BR> 1DRG NCB 18 -
0.326 -0.229 -0.603<BR> 1DRG
HAF 19 -0.405 -0.241
-0.543<BR> 1DRG CCA 20
-0.206 -0.185 -0.563<BR> 1DRG
OBF 21 -0.113 -0.159
-0.640<BR> 1DRG CBZ 22
-0.187 -0.168 -0.413<BR> 1DRG
CBE 23 - 0.126 -0.302
-0.370<BR> 1DRG CAO 24
-0.241 -0.394 -0.332<BR> 1DRG
OAF 25 -0.338 -0.339
-0.274<BR> 1DRG OAP 26
-0.230 -0.514 -0.360<BR> 1DRG
NBY 27 -0.106 -0.046
-0.388<BR> 1DRG HAE 28 -
0.084 0.000 -0.473<BR> 1DRG
CBX 29 -0.062 0.009
-0.273<BR> 1DRG OBD 30
-0.012 0.122 -0.272<BR> 1DRG
CBW 31 -0.067 -0.063
-0.137<BR> 1DRG CBC
32 0.078 -0.071 -0.084<BR>
1DRG CAN 33 0.164 -0.170
-0.163<BR> 1DRG CBB
34 0.089 -0.114 0.063<BR>
1DRG NBV 35 -0.154 0.013
-0.045<BR> 1DRG HAD 36
-0.131 0.111 -0.043<BR> 1DRG
CBU 37 -0.254 -0.032
0.032<BR> 1DRG OBA 38 -
0.296 0.039 0.123<BR> 1DRG
CBT 39 -0.315 -0.174
0.014<BR> 1DRG CAZ 40
-0.241 -0.277 0.099<BR> 1DRG
CAL 41 -0.206 -0.403
0.018<BR> 1DRG CAE 42
-0.326 -0.495 -0.002<BR> 1DRG
CAM 43 - 0.094 -0.481
0.088<BR> 1DRG NBS 44
-0.452 -0.166 0.069<BR> 1DRG
HAC 45 -0.449 -0.181
0.167<BR> 1DRG CBR 46
-0.575 -0.144 0.017<BR> 1DRG
OAY 47 -0.666 -0.135
0.100<BR> 1DRG CBQ 48 -
0.618 -0.126 -0.131<BR> 1DRG
CAX 49 -0.520 -0.056
-0.228<BR> 1DRG CAJ 50
-0.533 0.096 -0.242<BR> 1DRG
CAD 51 -0.499 0.173
-0.114<BR> 1DRG CAK 52
-0.673 0.137 -0.289<BR> 1DRG
NBP 53 - 0.666 -0.245
-0.201<BR> 1DRG HAB 54
-0.595 -0.302 -0.244<BR> 1DRG
C 55 -0.797 -0.274
-0.207<BR> 1DRG O
56 -0.872 -0.267 -0.109<BR> 1DRG
CA 57 -0.856 -0.322
-0.340<BR> 1DRG CB
58 - 0.777 -0.276 -0.463<BR> 1DRG
CG 59 -0.821 -0.140
-0.516<BR> 1DRG CD
60 -0.725 -0.105 -0.629<BR> 1DRG
OE2 61 -0.635 -0.023
-0.602<BR> 1DRG OE1 62
-0.741 -0.164 -0.738<BR> 1DRG
N 63 - 0.871 -0.467
-0.358<BR> 1DRG HAA 64
-0.795 -0.522 -0.325<BR> 1DRG
CBL 65 -0.981 -0.519
-0.414<BR> 1DRG OAU 66
-1.093 -0.467 -0.410<BR> 1DRG
CBK 67 -0.968 -0.654
-0.484<BR> 1DRG CCT 68 -
0.833 -0.725 -0.469<BR> 1DRG
CCS 69 -0.860 -0.875
-0.449<BR> 1DRG CCR 70
-0.929 -0.913 -0.316<BR> 1DRG
CCQ 71 -0.842 -0.888
-0.192<BR> 1DRG CCP 72
-0.880 -0.760 -0.116<BR> 1DRG
CCO 73 - 0.763 -0.714
-0.029<BR> 1DRG CCN 74
-0.792 -0.577 0.034<BR> 1DRG
CCM 75 -0.676 -0.523
0.119<BR> 1DRG CCL 76
-0.670 -0.578 0.263<BR> 1DRG
CCK 77 -0.593 -0.710
0.282<BR> 1DRG CCJ 78 -
0.440 -0.698 0.279<BR> 1DRG
CCI 79 -0.385 -0.625
0.402<BR> 1DRG CCH 80
-0.232 -0.622 0.401<BR> 1.51200
1.51200 1.51200<BR>Thank you very
much!</SPAN></P></DIV></BLOCKQUOTE></BODY></HTML>