Hello Justin,<br><br>I created structure file for a 4-carbon repeating unit as follows:<br>HETATM 1 CAA DRG 1 14.260 -4.270 0.000 1.00 20.00 C<br>HETATM 2 1HAA DRG 1 14.175 -3.426 0.530 1.00 20.00 H<br>
HETATM 3 2HAA DRG 1 15.050 -4.790 0.326 1.00 20.00 H<br>HETATM 4 3HAA DRG 1 14.385 -4.045 -0.966 1.00 20.00 H<br>HETATM 5 CAB DRG 1 12.990 -5.110 0.170 1.00 20.00 C<br>
HETATM 6 1HAB DRG 1 12.205 -4.581 -0.153 1.00 20.00 H<br>HETATM 7 2HAB DRG 1 12.871 -5.326 1.139 1.00 20.00 H<br>HETATM 8 CAC DRG 1 13.070 -6.410 -0.620 1.00 20.00 C<br>
HETATM 9 1HAC DRG 1 13.855 -6.939 -0.297 1.00 20.00 H<br>HETATM 10 2HAC DRG 1 13.189 -6.194 -1.589 1.00 20.00 H<br>HETATM 11 CAD DRG 1 11.800 -7.250 -0.450 1.00 20.00 C<br>
HETATM 12 1HAD DRG 1 11.885 -8.094 -0.980 1.00 20.00 H<br>HETATM 13 2HAD DRG 1 11.675 -7.475 0.516 1.00 20.00 H<br>HETATM 14 3HAD DRG 1 11.010 -6.730 -0.776 1.00 20.00 H<br>
<br>I renamed the atoms and removed one hydrogen atoms from both ends to get repeating unit. CH2CH2, <br><br>1- I am not able to produce the repeating unit C2H4 in PRODRG. It adds the third H automatically. I dont know anyother way but removing the third H from structure file by hand..<br>
<br>Then I mesaured the C1 To C4 distance which is 0.388 A.<br><br>editconf -f prodrg.pdb -o prodrg.gro -box 0.388 -bt cubic<br><br> 12<br> 1DRG C1 1 0.208 0.006 0.242<br> 1DRG H11 2 0.158 0.010 0.328<br>
1DRG H12 3 0.149 -0.030 0.170<br> 1DRG C2 4 0.255 0.148 0.203<br> 1DRG H21 5 0.305 0.143 0.116<br> 1DRG H22 6 0.314 0.184 0.274<br> 1DRG C3 7 0.133 0.240 0.186<br>
1DRG H31 8 0.083 0.245 0.272<br> 1DRG H32 9 0.074 0.204 0.114<br> 1DRG C4 10 0.179 0.382 0.147<br> 1DRG H41 11 0.239 0.418 0.218<br> 1DRG H42 12 0.230 0.378 0.060<br>
0.38800 0.38800 0.38800<br><br>then : genconf -f prodrg.gro -o rep.gro -nbox 1 5 1<br><br>2- The problem here is that one CH2 unit with 2 H atoms is falling on the next repeating unit in the next box. i.e 4 H atoms and C atoms are overlapping... as shown below:<br>
<br> H H H <b>H H</b> H H H <br> | | | | | | | |<br> C-C-C-<b>CC</b>-C-C-C <br> | | | | | | | |<br> H H H <b>H H</b> H H H <br><br>Do you think I should use -d option? <br><br>Please guide me..<br>Thanks<br><br><br>