AMBER Archive (2004)

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

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Thu Jul 01 2004 - 00:02:17 CDT

To : Dear Amber8 professionals
 
Hi again,

I am quite new to LEAP. Could you please be more specific on steps
for creating my own library for BDG and NEB residues?
  
Best regards,
  
Jenk.

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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