Davide,
Thanks for your quick response. I tried that line but I got the error:
mdfil: Error unknown flag: min1.rst
usage: sander [-O|A] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
[-ref refc -x mdcrd -v mdvel -e mden -idip inpdip -rdip
rstdip -mdip mddip -ng numgroup -remlog remlog -rem [0|1|2] -inf mdinfo
-radii radii]Consult the manual for additional options.
other suggestions are welcome.
Lili
On 7/16/07, Davide Moiani <moiani.scripps.edu> wrote:
>
> Hi ,
> when you use a restrain and you have ntr=1 sander request you -ref .crd
>
> $AMBERHOME/exe/sander.1cpu -O -i min1.in -o min1.out -p taxol.prmtop -c
> -r min1.rst -ref taxol.inpcrd
> Can you try that line if it works.
>
> Davide
>
>
>
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> >Date: Mon, 16 Jul 2007 16:56:11 -0700
> >From: "Lili Peng" <lilipeng.gmail.com>
> >To: amber.scripps.edu
> >Subject: AMBER: refc error
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> >Dear all,
> >
> >I am having trouble running a restrained energy minimization on an
> organic
> >molecule. When I try to run it in Sander, I type in:
> >
> >" $AMBERHOME/exe/sander.1cpu -O -i min1.in -o min1.out -p taxol.prmtop -c
> >taxol.inpcrd -r min1.rst "
> >
> >My min1.in consists of:
> >
> >" Initial minimization of structure
> >&cntrl
> > imin=1, maxcyc=200,
> > ntpr=10,
> > ntr=1,
> > ibelly=1,
> > bellymask=':1-20',
> >/
> >"
> >However, when I try running the minimization, I get the error:
> >" Unit 10 Error on OPEN: refc"
> >
> >I Googled this problem, and I get some hits about specifying a refc file.
> >How do I go about doing so?
> >
> >Thanks in advance,
> >Lili
>
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Received on Wed Jul 18 2007 - 06:07:35 PDT
