Hello Justin,<br><br>I spent a full day to find a proper value for -d but it seems there is no way of getting correct bond lenght and angle at the same time. With the following commands I am getting correct bond length for the atoms connecting two monomer units but the angle is 140. I get 110 angle only when bond distance is much less than actual value (1.53 A). I have also tried monomer units with 6, 8, 10 carbon atoms. For 8 and 10 cases I can not even align carbons with the axis using princ. This proper geometry problem seems to be a very simple thing to figure out but I have reached no results. I would like you to provide me with a hint or suggestion...I appreciate your help. Thanks.<br>
<br>Great Red Owns Many ACres of Sand <br> 4<br> 1Eth C1 1 0.462 0.285 0.269<br> 1Eth C2 2 0.325 0.216 0.269<br> 1Eth C3 3 0.213 0.321 0.269<br> 1Eth C4 4 0.075 0.255 0.269<br>
0.53817 0.53817 0.53817<br><br>editconf -f 4C.pdb -o 4Cd-princ.gro -princ -d 0.075 -bt cubic<br>genconf -f 4Cd-princ.gro -o 4Cd-rep.gro -nbox 5 1 1<br><br>4Cd-rep.gro: replicated units:<br><br>Great Red Owns Many ACres of Sand <br>
20<br> 1Eth C1 1 0.462 0.285 0.269 0.0000 0.0000 0.0000<br>
1Eth C2 2 0.325 0.216 0.269 0.0000 0.0000 0.0000<br>
1Eth C3 3 0.213 0.321 0.269 0.0000 0.0000 0.0000<br> 1Eth C4 4 0.075 0.255 0.269 0.0000 0.0000 0.0000<br> 2Eth C1 5 1.000 0.285 0.269 0.0000 0.0000 0.0000<br> 2Eth C2 6 0.863 0.216 0.269 0.0000 0.0000 0.0000<br>
2Eth C3 7 0.751 0.321 0.269 0.0000 0.0000 0.0000<br> 2Eth C4 8 0.613 0.255 0.269 0.0000 0.0000 0.0000<br> 3Eth C1 9 1.538 0.285 0.269 0.0000 0.0000 0.0000<br> 3Eth C2 10 1.401 0.216 0.269 0.0000 0.0000 0.0000<br>
3Eth C3 11 1.289 0.321 0.269 0.0000 0.0000 0.0000<br> 3Eth C4 12 1.151 0.255 0.269 0.0000 0.0000 0.0000<br> 4Eth C1 13 2.077 0.285 0.269 0.0000 0.0000 0.0000<br> 4Eth C2 14 1.940 0.216 0.269 0.0000 0.0000 0.0000<br>
4Eth C3 15 1.828 0.321 0.269 0.0000 0.0000 0.0000<br> 4Eth C4 16 1.690 0.255 0.269 0.0000 0.0000 0.0000<br> 5Eth C1 17 2.615 0.285 0.269 0.0000 0.0000 0.0000<br> 5Eth C2 18 2.478 0.216 0.269 0.0000 0.0000 0.0000<br>
5Eth C3 19 2.366 0.321 0.269 0.0000 0.0000 0.0000<br> 5Eth C4 20 2.228 0.255 0.269 0.0000 0.0000 0.0000<br> 2.69085 0.53817 0.53817<br><br><input type="hidden"><input type="hidden"><div>
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