Hello Justin, I created structure file for a 4-carbon repeating unit as follows: HETATM 1 CAA DRG 1 14.260 -4.270 0.000 1.00 20.00 C HETATM 2 1HAA DRG 1 14.175 -3.426 0.530 1.00 20.00 H HETATM 3 2HAA DRG 1 15.050 -4.790 0.326 1.00 20.00 H HETATM 4 3HAA DRG 1 14.385 -4.045 -0.966 1.00 20.00 H HETATM 5 CAB DRG 1 12.990 -5.110 0.170 1.00 20.00 C HETATM 6 1HAB DRG 1 12.205 -4.581 -0.153 1.00 20.00 H HETATM 7 2HAB DRG 1 12.871 -5.326 1.139 1.00 20.00 H HETATM 8 CAC DRG 1 13.070 -6.410 -0.620 1.00 20.00 C HETATM 9 1HAC DRG 1 13.855 -6.939 -0.297 1.00 20.00 H HETATM 10 2HAC DRG 1 13.189 -6.194 -1.589 1.00 20.00 H HETATM 11 CAD DRG 1 11.800 -7.250 -0.450 1.00 20.00 C HETATM 12 1HAD DRG 1 11.885 -8.094 -0.980 1.00 20.00 H HETATM 13 2HAD DRG 1 11.675 -7.475 0.516 1.00 20.00 H HETATM 14 3HAD DRG 1 11.010 -6.730 -0.776 1.00 20.00 H
I renamed the atoms and removed one hydrogen atoms from both ends to get repeating unit. CH2CH2, 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.. Then I mesaured the C1 To C4 distance which is 0.388 A. editconf -f prodrg.pdb -o prodrg.gro -box 0.388 -bt cubic 12 1DRG C1 1 0.208 0.006 0.242 1DRG H11 2 0.158 0.010 0.328 1DRG H12 3 0.149 -0.030 0.170 1DRG C2 4 0.255 0.148 0.203 1DRG H21 5 0.305 0.143 0.116 1DRG H22 6 0.314 0.184 0.274 1DRG C3 7 0.133 0.240 0.186 1DRG H31 8 0.083 0.245 0.272 1DRG H32 9 0.074 0.204 0.114 1DRG C4 10 0.179 0.382 0.147 1DRG H41 11 0.239 0.418 0.218 1DRG H42 12 0.230 0.378 0.060 0.38800 0.38800 0.38800 then : genconf -f prodrg.gro -o rep.gro -nbox 1 5 1 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: H H H *H H* H H H | | | | | | | | C-C-C-*CC*-C-C-C | | | | | | | | H H H *H H* H H H Do you think I should use -d option? Please guide me.. Thanks
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