From owner-chemistry@ccl.net Mon Oct 15 03:19:00 2007
From: "Sina T reli sinatureli:_:gmail.com" <owner-chemistry~!~server.ccl.net>
To: CCL
Subject: CCL: Large Computation Time Leap in Mopac and A Question About pm6
Message-Id: <-35381-071015031546-8853-y0BoHQIMTg6YJrjtnADDhQ~!~server.ccl.net>
X-Original-From: "Sina  T  reli" <sinatureli:_:gmail.com>
Date: Mon, 15 Oct 2007 03:15:42 -0400


Sent to CCL by: "Sina  T  reli" [sinatureli!^!gmail.com]

Hello, have two questions mainly regarding mopac.

1- Can mndo parameters in a molecular modelling program be replaced with mndo/d and pm6 parameters. Or in another words are the functions used in these three methods the same and only the parameters different?

2- I am using mopac2007 to do some geometry optimizations with mndod and pm6. My first subject was a molecule of size 141 which was handled quite nicely and fast and ended about in 30 minutes. However when I added a ligand that was about of 20 atoms in size, the calculation time leaped to like 2 days. The cycles werent even initiated before half a day passed... I used .mopac as the first output file and when I wanted to optimized the ligated one I used .xyz format with some atoms fixed to their coordinates. Is there something I am doing wrong or is this leap expected? And also I read that mopac 2007 isnt very practical for molecules of size above 600. Say if I use it for a molecule of size 400 atoms would it take too long on a 3.8 ghz 1gb ram machine? (I might plan to continue the work in a advanced computational center then...)

Thanks