Re: 2 questions

From: Simon Cross <>
Date: Fri 17 Nov 2000 09:40:57 +0000 (GMT)

I usually find that a script file that removes all hydrogens is the best
option, as other software that I use names them slightly differently in
the pdb. You also need to check all the TER's are in the right place and
that the terminal oxygen is called OXT (as mentioned by David below).

Hope this helps,


Simon Cross
School of Chemistry
University of Nottingham
tel. 0115 9514193

On Thu, 16 Nov 2000, David Case wrote:

> 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
> --
> ==================================================================
> David A. Case | e-mail:
> Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
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Received on Fri Nov 17 2000 - 01:40:57 PST
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