<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Hi ALL,<br><br>I have a protein pdb file generated using MODELLER. When I use the pdb2gmx command on it, it throws the error:<br><br>Atom -C not found in residue MET1 while adding hydrogens<br>and<br>Atom OXT in residue LEU 404<br><br>The initial and end of the pdb file is like this:<br>---------------------------------------------------------------------------------<br>CRYST1 116.083 116.083 116.083 90.00 90.00 90.00 P 1 1<br>ATOM 1 N MET X 1 67.960 51.279 76.751 1.00 0.00 <br>ATOM 2 CA MET X 1 67.510
49.899 76.451 1.00 0.00 <br>ATOM 3 CB MET X 1 65.990 49.769 76.661 1.00 0.00 <br>ATOM 4 CG MET X 1 65.570 49.959 78.111 1.00 0.00 <br>ATOM 5 SD MET X 1 63.780 49.819 78.401 1.00 0.00 <br>ATOM 6 CE MET X 1 63.370 51.379 77.561 1.00
0.00 <br>ATOM 7 C MET X 1 67.840 49.539 75.041 1.00 0.00 <br>ATOM 8 O MET X 1 68.870 49.949 74.511 1.00 0.00 <br>ATOM 9 N ALA X 2 66.970 48.749 74.401 1.00 0.00 <br>ATOM 10 CA ALA X 2 67.240 48.349 73.051 1.00
0.00 <br>ATOM 11 CB ALA X 2 66.160 47.429 72.461 1.00 0.00 <br>ATOM 12 C ALA X 2 67.290 49.579 72.221 1.00 0.00 <br>.<br>.<br>.<br>ATOM 3069 OD2 ASP X 403 43.890 88.349 36.411 1.00 0.00 <br>ATOM 3070 C ASP X 403 42.590 84.299 34.251 1.00 0.00 <br>ATOM 3071 O ASP X 403
41.820 84.059 33.321 1.00 0.00 <br>ATOM 3072 N LEU X 404 42.790 83.449 35.281 1.00 0.00 <br>ATOM 3073 CA LEU X 404 42.100 82.199 35.401 1.00 0.00 <br>ATOM 3074 CB LEU X 404 42.250 81.559 36.791 1.00 0.00 <br>ATOM 3075 CG LEU X 404 43.710 81.209 37.151 1.00 0.00 <br>ATOM 3076
CD1 LEU X 404 44.580 82.469 37.241 1.00 0.00 <br>ATOM 3077 CD2 LEU X 404 43.770 80.349 38.431 1.00 0.00 <br>ATOM 3078 C LEU X 404 40.610 82.469 35.201 1.00 0.00 <br>ATOM 3079 O LEU X 404 40.010 81.799 34.311 1.00 0.00 <br>ATOM 3080 OXT LEU X 404 40.050 83.329 35.931 1.00
0.00<br>END<br>--------------------------------------------------------------------------------------<br><br>How can I remove these errors? Do I need to modify the pdb file anyway?<br>Any suggestion is welcome.<br><br>Regards,<br><br><div><font color="#0000bf" size="4"></font> </div><div style="color: rgb(0, 0, 191);"><strong>Anirban Ghosh</strong></div><div style="color: rgb(0, 0, 191);"><strong>Grade Based Engineer<br>Bioinformatics Team<br>Centre for Development of Advanced Computing (C-DAC)<br>Pune, India<br></strong></div></td></tr></table><br>
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