AMBER Archive (2008)

Subject: Re: AMBER: problems of antechamber

From: Junmei Wang (junmwang_at_gmail.com)
Date: Thu Jan 17 2008 - 23:24:52 CST

Hi,
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

Best

Junmei

On Jan 17, 2008 8:15 PM, liu junjun <ljjlp03_at_gmail.com> 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
>


  • application/octet-stream attachment: ihp.prepi
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