Date: Thu, 16 Nov 2000 07:55:35 -0800
From: David Case
Subject: Re: 2 questions

On Wed, Nov 15, 2000, wrote:

> ...When
> AMBER reads the pdb, it seems to put extra atoms on terminal groups; the
> extra atoms do not have a noticeable TYPE.

This probably (almost certainly?) means your pdb file has atom names in
the terminal residues that LEaP does not recognize. The most obvious
things to look for are an "H" in the first residue (by default, the three
protons bonded to the terminal nitrogen are named "H1", "H2", "H3") and
some name other than "OXT" for the second carboxyl oxygen at the C-terminus.

What you did sounds OK, but better would be to modify your original pdb file
to use the names Amber is expecting to see.

(When LEaP finds atom names it does not recognize, it adds these as extra
atoms, without any TYPE or other information. This is sometimes what you
want it to do, such as if you had a genuinely new type of resdiue. But
generally it just means that the pdb file needs some editing.)

...hope this helps...dac