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
_________________________________________________________________
-----------------------------------------------------------------
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
__________________________________________________________________
------------------------------------------------------------------
Received on Tue Jan 07 2003 - 07:55:31 PST
