<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Hi,<br> After long try and error and with some reference I made a topology of DMF with six site interaction using OPLS/AA and topolgen. Can some tell me is it the correct format of a topology file or do i need to consider any other fact.<br><br>;<br>; OPLS-AA topology, built by TopolGen version 1.0 (3/21/2009)<br>; Script written by: Justin Lemkul (jalemkul@vt.edu)<br>; This is your molecule's topology<br>; Check it carefully for any errors. It is not necessarily perfect!<br>;<br>; Topology written on Sun Sep 6 15:41:15 IST 2009<br>;<br>; Include force field<br>#include "ffoplsaa.itp"<br>[ atomtypes ]<br>C3 15.03500
0.285 A 3.80000e-01 7.11280e-01<br>N 14.00670 -0.570 A 3.25000e-01 7.11280e-01<br>C 12.01100 0.500 A 3.80000e-01 4.81160e-01<br>H 1.00800 0.020 A 2.50000e-01 1.25520e-01<br>O 15.99940 -0.500 A 2.96000e-01 8.78640e-01<br><br>[ moleculetype ]<br>; Name
nrexcl<br>DMF 3<br><br>[ atoms ]<br>; nr type resnr residue atom cgnr charge mass typeB chargeB massB<br> 1 C3 1 DMF CM1 1 0.285 12.01100 <br> 2 N 1 DMF NM 1
-0.570 14.00670 <br> 3 C3 1 DMF CM2 1 0.285 12.01100 <br> 4 C 1 DMF CF 1 0.500
12.01100 <br> 5 H 1 DMF HF 1 0.020 1.00800 <br> 6 O 1 DMF OF 1 -0.500 15.99940 <br><br>[
bonds ]<br>; ai aj funct<br> 1 2 1 0.14490 282001.6<br> 2 3 1 0.14490 282001.6<br> 2 4 1 0.13350 410032.0<br> 4 5 1 0.10900 284512.0<br> 4 6 1 0.12290 476976.0<br><br>[ pairs ]<br>; ai aj funct<br> 1 5 1<br> 1
6 1<br> 3 5 1<br> 3 6 1<br><br>[ angles ]<br>; ai aj ak funct<br> 1 2 3 1 116.200 711.280<br> 1 2 4 1 121.900 418.400<br> 3 2 4 1 121.900 418.400<br> 2 4 5 1 109.500
292.880<br> 2 4 6 1 122.900 669.440<br> 5 4 6 1 123.000 292.880<br><br>[ dihedrals ]<br>; ai aj ak al funct<br> 1 2 4 5 3 -0.29079 -0.87237 0.00000 1.16315 0.00000 0.00000<br> 1 2 4 6 3 25.47638 0.00000 -25.47638 0.00000 0.00000
0.00000<br> 3 2 4 5 3 -0.29079 -0.87237 0.00000 1.16315 0.00000 0.00000<br> 3 2 4 6 3 25.47638 0.00000 -25.47638 0.00000 0.00000 0.00000<br><br>[ dihedrals ]<br>; aj ak ai al funct<br> 1 3 2 4 1 improper_Z_N_X_Y<br> 2 6 4 5 1 improper_O_C_X_Y<br><br>[ system ]<br>;
Name<br>DMF, generated by TopolGen<br><br>[ molecules ]<br>; Compound #mols<br>DMF 1<br><br>Thanks<br>abhishek<br></td></tr></table><br>
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