AMBER Archive (2003)

Subject: Small organic molecules

From: Dvira Segal (dvira_at_post.tau.ac.il)
Date: Tue Jan 07 2003 - 09:55:31 CST

My question is about building small organic molecules in xleap and doing
energy minimization on them using Amber7. For example I tried building
Butane: eclipsed, gauge and anti in xleap and then doing energy
minimization. I used the file

min.in
------
  min (no shake, periodic) - just enough to relax for md
 &cntrl
  imin = 1, maxcyc = 500, nrun = 0, nsnb = 25,
  ntc = 1, ntf = 1, idiel = 1,
  scee = 2.0,
 &end

and then the command

sander -O -i min.in -p butane.top -c butane.crd -o butane.out
-r butane.rst

I got the error message:
-----------
namelist read: variable not in namelist
apparent state: unit 5 named min.in
last format: list io
lately reading sequential formatted external IO
run1: line 2: 20428 Aborted (core dumped) sander -O -i
min.in -p tbutane.top -c tbutane.crd -o tbutane.out -r tbutane.rst
-----------

What can be the problem?
What should I do for minimization of small organic molecules?
Do you have any example which demonstrate how to study small molecules?

Thank you,
 Dvira Segal

_________________________________________________________________
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 Dvira Segal
 School of Chemistry, Tel Aviv University
 Tel Aviv, 69978 ISRAEL

 Phone: 972-3-640 7634 Fax: 972-3-642 3765
 email: dvira_at_post.tau.ac.il
 http://femto.tau.ac.il/~dvira
__________________________________________________________________
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