AMBER Archive (2007)

Subject: Re: AMBER: Using ntr=1 in xleap

From: Lili Peng (lilipeng_at_gmail.com)
Date: Tue Sep 04 2007 - 17:23:59 CDT

Thanks! that worked.

On 8/31/07, Carlos Simmerling <carlos.simmerling_at_gmail.com> wrote:
>
> you need to set -ref <file> in the sander script.
> <file> is the coordinates that you want as the reference for the
> restraints.
>
> On 8/31/07, Lili Peng <lilipeng_at_gmail.com> wrote:
> >
> > 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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