> I want to make a restraint to a water molecule and have made some bond and
> angle parameters to keep it in place but I have a problem to give the
> correct argument for that specific water molecule. In my pdb it has residue
> number 220(after having remade it with tleap so the N-terminal is correctly
> numbered from 1) so I thought that I could make the bond like this
>
> bond 3NKN.222.O 3NKN.214.MG
>
> but this is apparently another water molecule because the minimisation
> breaks down and I see a water molecule trying to go through a residue in
> order to take place of the crystal water I want to keep - how can I make
> sure it is the correct water molecule?
An alternative way of getting residue numbers is to use ambpdb to
get a pdb from .top and inpcrd. Not sure why leap would savepdb with
different res numbers, but it is more object-oriented, which style
cares less about sequential ordering :-)
Bill
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Received on Sun Sep 19 2010 - 14:00:04 PDT
