Re: AMBER: problems of antechamber

From: Junmei Wang <>
Date: Thu, 17 Jan 2008 23:24:52 -0600

For your molecule, I have no problem to generate the correct prepi file,
although it is highly charged molecule. Which version of antechamber did
you use? I also attached the prepi file with this email



On Jan 17, 2008 8:15 PM, liu junjun <> wrote:

> Dear Amber:
> Thanks for your program of antechamber.
> I have encountered a question the day before yesterday when I
> used the antechamber to prepare the prepi file of a small molecular
> which is high-charged with -6 electrons. I assigned the am1-bcc
> charges to the molecular and the error information is that:
> 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
> However the prepi file can be made by antechamber. But when I do
> the molecular dynamic simmulation, the small molecular cannot be
> minimized normally, two atoms bumped with each other. The item of 1-4
> EEL = ************
> Now I give you the mol2 file of this molecular for your check.
> With best regards.
> Xi Chen
> College of Chemistry, Huazhong Normal University
> Wuhan, 430079, China

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to

Received on Sun Jan 20 2008 - 06:07:22 PST
Custom Search