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<div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><font face="Tahoma" size="2">On Friday, May 29, 2009 9:38:00 AM, </font><font face="Tahoma" size="2">vivek sharma <viveksharma.iitb@gmail.com> wrote:</font><br>> Thanks a lot for your quick response. It is really encouraging to get response from developers like you.<br>> <br>> I tried generating topology again with the same command line and corrected input file. This time I am<br>> getting error as <br>>
_________________<br>> <font face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size="2">Fatal error.<br></font>> <font face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size="2">Source code file: readmol2.c, line: 693<br></font>> <font face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size="2">Atom 4 (N) has 3 connections when allowed 0<br></font>> <font face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size="2">--------------------------------------------------------<br>
</font>> <br>> <font face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size="2">I tried with different forcefield but getting the same error. Is
there any misake on my part or<br></font>> <font face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size="2">molecule structure or topolbuild can't
handle such files ?<br></font>><br>> <font face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size="2">Please suggest if there is some other option for generating topology files from structure files.</font><br><br>I'm sorry. I had missed this before. Is there some reason why the<br>types of the C and N atoms are incomplete? Where did this file<br>come from? The absence of correct atom types is indeed an error.<br><br>All carbons must have a complete type that is one of<br>C.3, C.2, C.cat , <a rel="nofollow" target="_blank" href="http://C.ar">C.ar</a>, or C.1<br>All nitrogens must have a complete type that is one of<br>N.3, N.2, N.1, <a rel="nofollow" target="_blank" href="http://N.ar">N.ar</a>, N.pl3, <a rel="nofollow" target="_blank" href="http://N.am">N.am</a>, or N.4<br>All oxygens must have a complete type that is one of<br>O.3, O.2, or O.co2<br>All sulfurs must have a complete type that is one of<br>S.3, S.2,
S.o, or S.o2<br>The only phosphorous type is P.3<br>The only other sub-typed elements have the types<br>Co.oh, Cr.oh, and Cr.th<br><br>topolbuild can handle syntactically correct mol2 files. The key phrase is<br>syntactically correct. It means that the file must match the definition for<br>mol2 files given by Tripos in
terms of atom types, as well as bond types<br>and format. topolbuild uses the Tripos atom types as part of the<br>assignment of gaff, amber, gromacs, or (version 1.3 now in testing)<br>oplsaa atom types.<br><br>I have tried to guess at the correct Tripos atom types for your molecule<br>based on the bonding and I attach that below. These may not be absolutely<br>correct. However, this does generate a topology with topolbuild.<br><br>@<TRIPOS>MOLECULE<br>Bromo-WR99210.pdb<br> 42 43 0 0 0<br>SMALL<br>GASTEIGER<br>Energy = 0<br><br>@<TRIPOS>ATOM<br> 1 BR 3.8280 5.3090 11.2220 Br 1 UNK1 -0.0503<br> 2 O 0.1390 1.8570
3.5110 O.3 1 UNK1 -0.2127<br> 3 O 2.3680 3.2800 5.7230 O.3 1 UNK1 -0.4919<br> 4 N -0.7270 2.5300 2.6710 N.pl3 1 UNK1 -0.0823<br> 5 N -2.7920 2.6890 1.3630 N.ar 1 UNK1 -0.0643<br> 6 N -1.1590 4.4210 1.3650 N.ar 1
UNK1 -0.0011<br> 7 N 0.8240 4.2680 2.6030 N.pl3 1 UNK1 -0.2863<br> 8 N -3.1550 4.6100 0.1360 N.pl3 1 UNK1 -0.2859<br> 9 C -1.9520 1.8810 2.2650 C.3 1 UNK1 0.2652<br> 10 C -2.8030 1.5760 3.5030 C.3 1
UNK1 0.0108<br> 11 C -1.6250 0.5840 1.5150 C.3 1 UNK1 0.0108<br> 12 C -0.3810 3.7610 2.1840 C.2 1 UNK1 0.4233<br> 13 C -0.2000 2.2550 4.8340 C.3 1 UNK1 0.0932<br> 14 C 0.7110 1.5570 5.8320 C.3 1
UNK1 0.0086<br> 15 C -2.3690 3.8600 0.9790 C.2 1 UNK1 0.4286<br> 16 C 2.1760 1.8790 5.5870 C.3 1 UNK1 0.0918<br> 17 C 2.7000 3.7400 6.9700 C.ar 1 UNK1 0.1206<br> 18 C 3.4230 2.9260 7.8350 C.ar 1
UNK1 -0.0189<br> 19 C 2.3110 5.0170 7.3580 C.ar 1 UNK1 -0.0189<br> 20 C 3.7590 3.3940 9.1050 C.ar 1 UNK1 -0.0443<br> 21 C 2.6470 5.4860 8.6280 C.ar 1 UNK1 -0.0443<br> 22 C 3.3720 4.6740 9.5020 C.ar 1 UNK1
0.0181<br> 23 H -2.3890 0.7640 4.1100 H 1 UNK1 0.0301<br> 24 H -3.7980 1.2280 3.1950 H 1 UNK1 0.0301<br> 25 H -2.9770 2.4700 4.1120 H 1 UNK1 0.0301<br> 26 H -2.5380 0.0750 1.1850 H 1
UNK1 0.0301<br> 27 H -1.0580 -0.1150 2.1400 H 1 UNK1 0.0301<br> 28 H -1.0240 0.7890 0.6210 H 1 UNK1 0.0301<br> 29 H -1.2070 1.9930 5.1370 H 1 UNK1 0.0600<br> 30 H -0.1050 3.3420 4.9500 H
1 UNK1 0.0600<br> 31 H 0.5760 0.4730 5.7420 H 1 UNK1 0.0321<br> 32 H 0.4220 1.8490 6.8470 H 1 UNK1 0.0321<br> 33 H 2.8170 1.2260 6.1790 H 1 UNK1 0.0697<br> 34 H 2.4370 1.6350 4.5500
H 1 UNK1 0.0697<br> 35 H 1.1470 5.1760 2.2890 H 1 UNK1 0.2547<br> 36 H 1.4470 3.7330 3.1970 H 1 UNK1 0.2547<br> 37 H -2.8590 5.5250 -0.1840 H 1 UNK1 0.2548<br> 38 H -4.0520
4.2670 -0.1900 H 1 UNK1 0.2548<br> 39 H 3.8150 1.9500 7.5800 H 1 UNK1 0.0654<br> 40 H 1.7450 5.6510 6.6810 H 1 UNK1 0.0654<br> 41 H 4.3360 2.7560 9.7690 H 1 UNK1 0.0630<br> 42
H 2.3370 6.4850 8.9220 H 1 UNK1 0.0630<br>@<TRIPOS>BOND<br> 1 1 22 1<br> 2 2 4 1<br> 3 2 13 1<br> 4 3 16 1<br> 5 3 17 1<br> 6 4 9 1<br> 7 4 12 1<br>
8 5 9 1<br> 9 5 15 2<br> 10 6 12 2<br> 11 6 15 1<br> 12 7 12 1<br> 13 7 35 1<br> 14 7 36 1<br> 15 8 15 1<br> 16 8 37 1<br> 17 8 38 1<br> 18
9 10 1<br> 19 9 11 1<br> 20 10 23 1<br> 21 10 24 1<br> 22 10 25 1<br> 23 11 26 1<br> 24 11 27 1<br> 25 11 28 1<br> 26 13 14 1<br> 27 13 29 1<br> 28 13 30 1<br> 29
14 16 1<br> 30 14 31 1<br> 31 14 32 1<br> 32 16 33 1<br> 33 16 34 1<br> 34 17 18 ar<br> 35 17 19 ar<br> 36 18 20 ar<br> 37 18 39 1<br> 38 19 21 ar<br> 39 19 40 1<br> 40 20
22 ar<br> 41 20 41 1<br> 42 21 22 ar<br> 43 21 42 1<br>@<TRIPOS><br><br><div> </div>-- <br>Bruce D. Ray, Ph.D.<br>Associate Scientist, and Operations Director<br>NMR Center<br>IUPUI<br>Physics Dept.<br>402 N. Blackford St.<br>Indianapolis, IN 46202-3273</div></div></div><br>
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