On Mon, Mar 1, 2010 at 1:00 PM, Ivan Gladich <igladich.purdue.edu> wrote:
> Thank you Jason but it still does not work.
> I did like this
>
> ambpdb -p topol.pdb <restrt >my.pdb
I'm confused... Is topol.pdb a prmtop file or a pdb file? I don't
think ambpdb takes a pdb file as a topology file...
>
> translate -i my.pdb -f pdb -c translate -vx 0 -vy 0 -vz 20 -o initial.pdb
>
> ptraj <topol.pdb
> trajin initial.pdb
> trajout coord_trans [restrt]
I believe ptraj has to be supplied a topology file
ptraj prmtop < script
where script reads
trajin initial.pdb pdb
trajout coord_trans.inpcrd restart
Don't forget to put "pdb" after the trajin statement to let ptraj know
what format it is.
I don't think you're using ptraj (or ambpdb) correctly...
>
> Now the coordinates are translate in the z-axes and they are written in
> an unformatted way.So I fixed in the initialization file of sander the
> option ntx=2
ptraj should preserve formatting for a restart file (specify restart,
without [] above)
> Sander is not able to restart with the new coord_trans and with the old
> topol.pdb
> With this new coordinate file and it provides an error of
>
> At line 2216 of file _ew_setup.f
> Fortran runtime error: Bad value during floating point read
>
>
> Jason Swails wrote:
>> You could probably read it through ptraj.
>>
>> ------------------------------------------------------
>> trajin pdbfile pdb
>>
>> trajout inpcrd_file restart
>> ------------------------------------------------------
>>
>> Good luck!
>> Jason
>>
>> On Sun, Feb 28, 2010 at 5:17 PM, Ivan Gladich <igladich.purdue.edu> wrote:
>>> Thank you very much Jason.
>>> Now it works!
>>> Last question: if now I would like to come back to have an .inpcrd file
>>> with the translated coordinates but with the same topology topol.prmtop,
>>> what do I have to do?
>>> Thanks again
>>>
>>>
>>>
>>> Jason Swails wrote:
>>>> On Sun, Feb 28, 2010 at 2:00 PM, Ivan Gladich <igladich.purdue.edu> wrote:
>>>>> Dear all
>>>>> I have some problem to translate a restrt file.
>>>>> Indeed, after a constant pressure simulation, I would like to translate
>>>>> my system in my box to perform a constant volume simulation in a larger
>>>>> box.
>>>>> I have seen in the web that "translate" can do it but it wants a .pdb
>>>>> format file.
>>>>> For this reason I did
>>>>>
>>>>> $AMBERHOME/exe/ambpdb -p topol.prmtop <restrt > my.pdb
>>>>>
>>>>> after that I did
>>>>>
>>>>> $AMBERHOME/exe/translate -i my.pdb -vx 0 -vy 0 -vz 40 -o transl
>>>> translate -h
>>>>
>>>> will give you help. You're missing the "-f format" flag. Add -f pdb
>>>> to your command.
>>>>
>>>> Good luck!
>>>> Jason
>>>
>>> --
>>> -------
>>> Ivan Gladich, Ph.D.
>>>
>>> Dreyfus Postdoctoral Fellow
>>> Department of Chemistry
>>> Purdue University
>>> 560 Oval Drive, box 140
>>> West Lafayette
>>> IN 47906 USA
>>>
>>> Room: 265C
>>> Tel:765-494-5225
>>> e-mail: igladich.purdue.edu
>>> web page: http://web.ics.purdue.edu/~igladich/
>>>
>>> --------
>>>
>>> _______________________________________________
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>>>
>>
>>
>>
>
>
> --
> -------
> Ivan Gladich, Ph.D.
>
> Dreyfus Postdoctoral Fellow
> Department of Chemistry
> Purdue University
> 560 Oval Drive, box 140
> West Lafayette
> IN 47906 USA
>
> Room: 265C
> Tel:765-494-5225
> e-mail: igladich.purdue.edu
> web page: http://web.ics.purdue.edu/~igladich/
>
> --------
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Mar 01 2010 - 10:30:06 PST
