AMBER Archive (2004)

Subject: AMBER: problem with antechamber

From: Cai, Yufeng (Yufeng.Cai_at_umassmed.edu)
Date: Sun Oct 17 2004 - 21:04:28 CDT

Hi folks,

I am trying to use antechamber to generate a prep file for my chemical
compound from PDB structure and here is what I met:

 

When set the output as .ac, in the .ac file there are all my atoms
although some of them can not be recognized and set to "DU";

When set the output as prepi, it saids:

 

"Cannot successfully assign bond type for this molecule, please double
check the structure (the connectivity) and/or adjust atom valence
penalty parameters in APS.DAT"

 

And in the output (prepi) file, it only includes part of the compound's
atoms.

 

BTW, in my pdb files, there is no connected information. Is this
matters?

 

If anyone has experience with generating chemical compound parameters
with antechamber, please give me some advice. Thank you very much!

 

Yufeng

 

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