> 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.
I think CONECT records are ignored in any case.
You should put a TER 'card' (line) after each
residue that is not bonded to the one following,
so if there are no bonds to your ions you would
have e.g.
TER
ATOM <ion>
TER
ATOM <ion>
TER
> 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.
I can't help with that one..
Bill
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Received on Fri Aug 13 2010 - 13:30:23 PDT
