AMBER Archive (2007)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Aug 31 2007 - 16:49:14 CDT

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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