Oops sorry. Wrong quotes.
Thanks Jason.
Best,
Le 15/09/2010 14:55, Jason Swails a écrit :
> 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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>
>
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Received on Wed Sep 15 2010 - 07:00:03 PDT
