> cat myprot.pdb mylig.pdb> complex.pdb
It is possible that docking will be poor, e.g. atoms overlapping.
Usually people combine molecules in a graphics editor to get the
orientation right. In this case you are combining what appear to
be two solvated systems; normally one would dock molecules, then
solvate and equilibrate. This results in all the waters being at
the end of the crd/top files, enabling faster calcs, whereas in
your case the order will be mixed.
> FATAL: Atom .R.A does not have a type.
Usually this message has more information, including residue name
and atom name. Maybe if the setup is fixed, this message will go
away.
Bill
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Received on Mon Sep 14 2009 - 13:38:16 PDT
