On Fri, Aug 13, 2010, Ben Roberts wrote:
>
> 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.
We will need to know real details: what library did you use for the metal
cluster? exactly what commands did you give to tleap?
>
> 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 Ã )
> 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.
How do you know that tleap actually created the bonds? Did you use desc or
rdparm? Unless you use something like "bondbydistance", tleap won't make
bonds between atoms (again, unless those bonds are in some library file).
....dac
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Received on Fri Aug 13 2010 - 13:00:12 PDT
