AMBER Archive (2006)

Subject: Re: AMBER: modeling a non-standard molecule.

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed Mar 08 2006 - 15:19:21 CST

> ... when I put the molecule in the protein
> and try to crate the prmtop and inpcrd file, it gives me a bunch of
> warnings for missing parameters (inlcuding bond lengths, angles and
> finally torsions). I think most of these warnings come from the new
> bonds that I make between the molecule and the residues on either
> side.

Assuming the correct atoms are bonded AND of the correct type,
you will need to add the necessary parameters. Make sure the
bonds and types are correct first however!

Bill
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