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'
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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Received on Wed Sep 15 2010 - 06:00:04 PDT
