Hello Justin,
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.
Great Red Owns Many ACres of Sand
4
1Eth C1 1 0.462 0.285 0.269
1Eth C2 2 0.325 0.216 0.269
1Eth C3 3 0.213 0.321 0.269
1Eth C4 4 0.075 0.255 0.269
0.53817 0.53817 0.53817
editconf -f 4C.pdb -o 4Cd-princ.gro -princ -d 0.075 -bt cubic
genconf -f 4Cd-princ.gro -o 4Cd-rep.gro -nbox 5 1 1
4Cd-rep.gro: replicated units:
Great Red Owns Many ACres of Sand
20
1Eth C1 1 0.462 0.285 0.269 0.0000 0.0000 0.0000
1Eth C2 2 0.325 0.216 0.269 0.0000 0.0000 0.0000
1Eth C3 3 0.213 0.321 0.269 0.0000 0.0000 0.0000
1Eth C4 4 0.075 0.255 0.269 0.0000 0.0000 0.0000
2Eth C1 5 1.000 0.285 0.269 0.0000 0.0000 0.0000
2Eth C2 6 0.863 0.216 0.269 0.0000 0.0000 0.0000
2Eth C3 7 0.751 0.321 0.269 0.0000 0.0000 0.0000
2Eth C4 8 0.613 0.255 0.269 0.0000 0.0000 0.0000
3Eth C1 9 1.538 0.285 0.269 0.0000 0.0000 0.0000
3Eth C2 10 1.401 0.216 0.269 0.0000 0.0000 0.0000
3Eth C3 11 1.289 0.321 0.269 0.0000 0.0000 0.0000
3Eth C4 12 1.151 0.255 0.269 0.0000 0.0000 0.0000
4Eth C1 13 2.077 0.285 0.269 0.0000 0.0000 0.0000
4Eth C2 14 1.940 0.216 0.269 0.0000 0.0000 0.0000
4Eth C3 15 1.828 0.321 0.269 0.0000 0.0000 0.0000
4Eth C4 16 1.690 0.255 0.269 0.0000 0.0000 0.0000
5Eth C1 17 2.615 0.285 0.269 0.0000 0.0000 0.0000
5Eth C2 18 2.478 0.216 0.269 0.0000 0.0000 0.0000
5Eth C3 19 2.366 0.321 0.269 0.0000 0.0000 0.0000
5Eth C4 20 2.228 0.255 0.269 0.0000 0.0000 0.0000
2.69085 0.53817 0.53817
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