AMBER Archive (2009)

Subject: Re: [AMBER] parameterization of protein-ligand complex

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed Sep 09 2009 - 12:12:28 CDT

> 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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