AMBER Archive (2007)

Subject: AMBER: Using ntr=1 in xleap

From: Lili Peng (lilipeng_at_gmail.com)
Date: Fri Aug 31 2007 - 16:27:44 CDT

Hi all,

I'm having problems running a two-fold minimization procedure on a
20-residue polyglutamic acid structure. I'd like to 1) minimize the solvent
(TIP3PBOX) while keeping the polypeptide fixed and 2) minimize the entire
system. However, in my initial minimization of solvent, I run into the
error "Unit 10 Error on open: refc". I'm pretty sure the error has to do
with my setting ntr=1, because when i turn ntr off (=0), Sander executes the
minimization smoothly.

My input line for running Sander is: "/sander.1cpu -O -i min_classical.in
-o min_classical.out -p GLU20_alpha.prmtop GLU20_.inpcrd -r
min_classical.rst"

My minimization script is the following:

"Initial minimization of solvent
 &cntrl
 imin=1, maxcyc=200, ncyc=50, ntpr=10,
 cut=8.0, ntb=1, ntc=2,
 ntr=1, restraintmask=':1-20',
 restraint_wt=10.0
 /
"

Does anyone know what could the problem?

Thanks,

Lili


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