Yes, you are right, ambpdb reads only .prmtop
Now It works!
Thank you Janson!
If you pass in Indiana, I will offer you a beer
Thanks again
Ivan
Jason Swails wrote:
> 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/
>>>>
>>>> --------
>>>>
>>>> _______________________________________________
>>>> 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/
>>
>> --------
>>
>> _______________________________________________
>> 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 - 12:00:02 PST
