On Wed, Sep 15, 2010 at 8:33 AM, Baptiste Legrand <bap.legrand.gmail.com>wrote:
> Ok Thanks, all is fine. I calculate initial structures, minimize them
> and finally sa with NMR restraints.
> After the minimization, I try to create a script (linux) to
> automatically run sander on the multiple structures (min.rst.1,
> min.rst.2...to write sa.rst.1 sa.rst.2 ... respectively) but It fail:
> for x in 'seq 1 100'
>
what kind of quotes are you using here? Are they single quotes? This
should be the ` quote, not the '. What this is doing is setting x to "seq 1
100", so your command line is becoming
sander -O -i sa.in -o sa.out.seq 1 100 -c min.rst.seq 1 100 -p prmtop -r
sa.rst.seq 1 100 -x traj.seq 1 100
I believe. That's why mdfil is complaining about a flag "1" being
unrecognized. Notice the difference in quotes above.
Hope this helps,
Jason
do
> sander -O -i sa.in -o sa.out.$x -c min.rst.$x -p prmtop -r sa.rst.$x -x
> traj.$x
> done
> But I have this error message: /mdfil/: /Error unknown fla/g///: 1/ ...
> My script should not be good, what is the best way to do this operation?
> Thanks.
>
> Best regards,
> Baptiste
>
>
> Le 08/09/2010 19:06, Bill Ross a écrit :
> > ambpdb just uses restrt files as input.
> > You can use ptraj to convert each frame of mdcrd to pdb.
> > You may want to also view an animation of the mdcrd using e.g. VMD -
> > this is very instructive.
> >
> > Bill
> >
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Sep 15 2010 - 06:00:05 PDT
