Thank you Jason but it still does not work.
I did like this
ambpdb -p topol.pdb <restrt >my.pdb
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]
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
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/
>>
>> --------
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
--
-------
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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Received on Mon Mar 01 2010 - 10:30:02 PST
