Hello, I am trying to get the stream file for chlorophyll A. When i upload a mol2 file of chlorophyll A
CLA_fix.mol2.txt (13.6 KB)
to CGenFF, I get this error:
attype warning: element (Mg) not supported;
skipped molecule.
How can i fix this problem?
I wouldn’t trust any force fields, before thorough validation, when simulating a molecule with such a tightly coordinated ion. However, what you could try is to remove the magnesium ion before generating parameters with CGenFF. Then you have to carefully check the output, especially the partial charges of the nitrogen atoms. After that, you can just re-introduce the magnesium ion at the same coordinates in the gro file and add it as a separate [ molecules ] entry in the topology file. But, as I hinted at above, I would be surprised if the simulations produce any valid results.