Dear all,
Finally, is there a script (or a simple manner) available to extract
specifically the Etot and restraints lines of the last step in all the
"sa.out" files after the sa to select the most representative structures?
Thanks.
Best wishes,
Baptiste
Le 15/09/2010 15:36, Baptiste Legrand a écrit :
> 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 Thu Sep 16 2010 - 07:30:04 PDT
