Hi,
I've been trying to use leap to prepare a prmtop and an inpcrd from a PDB file containing a metalloprotein with, with three dinickel clusters.
I've encountered two odd problems.
The first is that both sleap and tleap seem to create spurious bonds between the two nickel ions, which are far enough apart (3.5 to 4 Å) that they shouldn't be bonded to each other. I've checked the file, and there are no CONECT records indicating that the two should be bonded.
The second is that, in sleap, the "deleteBond" command doesn't work. It doesn't cause a stoppage; it just gets skipped with "deletebond: command not found!" Thus, for the moment, I'm forced back to tleap.
Can anyone shed any light on what might be going on here?
Thanks,
Ben
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Received on Fri Aug 13 2010 - 13:00:06 PDT
