AMBER Archive (2006)

Subject: Re: AMBER: Problem in Antechamber

From: David A. Case (
Date: Thu Jan 12 2006 - 19:40:50 CST

On Tue, Jan 10, 2006, Sai Kumar Ramadugu wrote:

> I want to simulate a Drug-DNA complex. The complex has
> acridine-peptide (N-alpha(9-acridinoyl)-tetraarginine).
> Cannot successfully assign bond type for this molecule, please :
> (1) double check the structure (the connectivity) and/or
> (2) adjust atom valence penalty parameters in APS.DAT, and/or
> (3) increase MAXVASTATE in define.h and recompile bondtype.C

Try giving the "-j 5" flags to the antechamber command.

> The prepin created doesnot have atom names.

I have never seen this behavior. Can you post the pdb input file you used;
also the prepin file: what is put in place of the atom names?


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