Re: AMBER: PDB files

From: David A. Case <>
Date: Tue, 20 Jan 2004 15:12:04 -0800

On Tue, Jan 20, 2004, Beale, John wrote:

> I have been constructing small peptides (less than 30 residues) by using
> Sybyl 6.91 to build the molecules and generate the pdb files. If I try to
> read these pdb files into LEaP, the program throws up lots of error messages
> and will not produce the prmtop and inpcrd files. I have found that the only
> way to get the pdb files read into LEaP successfully is to manually edit the
> pdb files, putting the atoms in the same order in which they occur in the
> AMBER amino acid libraries.

We would need to see an example of a pdb file that doesn't work. The order
of atoms within a residue should be irrelevant: they do not need to be in
the same order as in the amino acid libraries. (For example, files from
the pdb (RCSB) itself are generally not in the "amber" order either.) I
wonder if your editing is not in fact making some other change as well (?)


David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Tue Jan 20 2004 - 23:53:01 PST
Custom Search