Dear all,
I have the cif file of the MOF structure, the atoms and their indexes goes like this:
C1 1.0 0.3521 0.68248 0.49724
Cr2 1.0 0.6727 0.73299 0.90674
C3 1.0 0.9812 0.86236 0.85294
C4 1.0 0.29174 0.5265 0.71863
...
C1185 1.0 0.17108 0.59341 0.61745
C1186 1.0 0.14289 0.58226 0.66194
C1187 1.0 0.1861 0.67126 0.70408
Cr1188 1.0 0.25915 0.66547 0.69122
...
But in the simulation, we divided the atoms to different types,e.g. only 3 types of carbon atom and 2 types of Cr and so on. The force field is made for the type of atoms such as:
C1 lennard-jones 47.8562 3.47299
C2 lennard-jones 47.8562 3.47299
Cr1 lennard-jones 7.54829 2.69319
Cr2 lennard-jones 7.54829 2.69319
So the data need to be like:
C1 1.0 0.3521 0.68248 0.49724
Cr2 1.0 0.6727 0.73299 0.90674
C1 1.0 0.9812 0.86236 0.85294
C2 1.0 0.29174 0.5265 0.71863
...
C1 1.0 0.17108 0.59341 0.61745
C1 1.0 0.14289 0.58226 0.66194
C2 1.0 0.1861 0.67126 0.70408
Cr2 1.0 0.25915 0.66547 0.69122
...
How do I change the atom index? There are too many atoms for me to do it manually. Is there any software that can do this ?
Openbabel conversions work to get cifs into a RASPA readable format.
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