Dear Dr. Case,
Thank you for the information and suggestions.
I will look for some other package to make the job done.
Thanks
Jagur
________________________________
From: David A Case <case.biomaps.rutgers.edu>
To: Jagur Lambix <jagurlambix.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Friday, August 19, 2011 12:54 PM
Subject: Re: [AMBER] antechamber + CNT parameter
On Fri, Aug 19, 2011, Jagur Lambix wrote:
> I am trying to create the parameter of a Carbon Nano Tube (CNT) using
> the antechamber.
> The CNT has 576 atoms in total.
Antechamber was not designed for such problems.
You can look at the sqm output (perhaps turn up debugging), but this is way
outside the design scope of antechamber, which is ordinary, moderate-sized
closed-shell organic molecules.
The point of asking for bcc charges is to get, well, atomic charges. But a
carbon nanotube probably has minimal polarity anyway. You are asking a
quantum program to minimize the geometry of a system with 3500 electrons, and
that is not going to happen (at least with our codes).
There are clues in your output:
> The atom number exceeds the MAXATOM, reallocate memory
> Info: the bond number exceeds MAXBOND, reallocate memory automatically
> Info: the atom number exceeds the MAXATOM, reallocate memory automatically
> Info: the actual number of rings (17792) exceeds the defaut ring size (500), reallocate memory automatically
> Info: the atom number exceeds the MAXATOM, reallocate memory automatically
> Info: the actual number of rings (17792) exceeds the defaut ring size (500), reallocate memory automatically
Antechamber is trying to resize itself to be big enough for your system, but
is not succeeding.
...dac
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Received on Fri Aug 19 2011 - 10:30:04 PDT
