AMBER Archive (2005)

Subject: RE: AMBER: antechamber problem

From: Junmei Wang (jwang_at_encysive.com)
Date: Tue Sep 20 2005 - 18:05:36 CDT

Hi,
Antechamber recognize element/atom type based on the atom names.
Therefore, you may manually modify the atom names, for example, change
AP to PA, A01 to O1A.

Best regards

Junmei

Hello, Amber:

I try to load a ligand (named as FAD-1 here), and use abtechamber to
creat prep file. Here is how I did:

guanine.1% setenv AMBERHOME /usr/local/amber7
guanine.2% antechamber -i FAD.pdb -fi pdb -o FAD.prep -fo prepi

 Unrecognized atomic name AP , exit
 Unrecognized atomic name AO1 , exit
 Unrecognized atomic name AO2 , exit
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I search the mail list, but hard to find the answer. I have included the
pdb file as an attachment. I use Amber7.

Thanks for any suggestion.

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