AMBER Archive (2004)

Subject: Re: AMBER: Problems with processing SYBYL-Tripos pdb files in LEAP

From: David A. Case (
Date: Wed Jun 30 2004 - 12:50:41 CDT

On Wed, Jun 30, 2004, Cenk Andac wrote:
> I am attaching a SYBYL pdb file (nea.pdb) for neamine (an aminoglycoside)
> for amber experts to see.
> Unknown residue: BDG number: 0 type: Terminal/beginning
> Unknown residue: NEB number: 1 type: Terminal/last

There are no residues named "BDG" or "NEB" in the glycam04 library. You
will have to create the library files yourself, presumably by modifying
some units that are already there. You can use the "edit" command in LEaP
to morph one residue into something similar (or something completely
different, but something similar is obviously to be preferred.)

...good luck....dac

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