The file must exist in the directory where you start sander, or must be
specified by location relative to that or your home directory: '-c
~/inpcrd' or root: ' -c /home/whatever/inpcrd'.
Bill
On 12/4/15 12:51 AM, Nikolay N. Kuzmich wrote:
> Hello again,
>
> nikolay/Tutorial% $AMBERHOME/bin/sander -O -i 01_Min.in -o 01_Min.out -p
> prmtop -c inpcrd -r 01_Min.rst -inf 01_Min.mdinfo
>
> Error opening unit 30: File "inpcrd" is missing or unreadable
>
> Actually, the inpcrd file does exist in folder
>
> /home/nikolay/amber14/dat/leap/prep/
>
> and is identical to inpcrd file of this tutorial available at
>
> http://ambermd.org/tutorials/basic/tutorial0/include/inpcrd
>
> The input file 01_Min.in is located at
>
> /home/nikolay/Tutorial/
>
> and is also identical to that one from
> Alanine_Dipeptide_Files.zip
> <http://ambermd.org/tutorials/basic/tutorial0/include/Alanine_Dipeptide_Tutorial_Files.zip>
> archive.
> So what can be a source of trouble again?
>
> Kind regards,
> Nick
>
> 2015-12-01 12:27 GMT+03:00 Nikolay N. Kuzmich <nnkuzmich.gmail.com>:
>
>> If I add a blank line at the end of 01_Min.in file,
>> another error message appears:
>> nikolay/Tutorial% $AMBERHOME/bin/sander -O -i 01_Min.in -o 01_Min.out -p
>> prmtop -c inpcrd -r 01_Min.rst -inf 01_Min.mdinfo
>>
>> Error opening unit 30: File "inpcrd" is missing or
>> unreadable
>> nikolay/Tutorial%
>>
>> Kind regards
>> Nick
>>
>>
>>
>> 2015-12-01 12:08 GMT+03:00 Nikolay N. Kuzmich <nnkuzmich.gmail.com>:
>>
>>> you might try without a space before the &cntrl and / lines
>>>
>>> On Mon, Nov 30, 2015 at 6:39 AM, Nikolay N. Kuzmich <nnkuzmich.gmail.com>
>>>
>>> wrote:
>>>
>>> *> Dear Bill, David and other Amber users, *
>>> *> *
>>> *> I enclose a copy of the 01_Min.in file. *
>>> *> How should it be formatted correctly?.. *
>>> *> Also an extra blank line at the end mdread1.F90 file was added, *
>>> *> but it didn't help. *
>>> *> So what can be done next?.. *
>>> *> I am a beginner at Amber and compiling, etc. *
>>> *> so hope for your empathy. *
>>> *> *
>>> *> Kind regards, *
>>> *> Nick *
>>> *> *
>>> *> 2015-11-27 11:28 GMT+03:00 Nikolay N. Kuzmich <nnkuzmich.gmail.com
>>> <http://nnkuzmich.gmail.com>>: *
>>> *> *
>>> *> > Dear Amber users, *
>>> *> > *
>>> *> > When I launched minimization procedure in course of the alanine
>>> dipeptide *
>>> *> > tutorial *
>>> *> > I have received an error message: *
>>> *> > *
>>> *> > linux-0bye nikolay/Tutorial# $AMBERHOME/bin/sander -O -i 01_Min.in
>>> -o *
>>> *> > 01_Min.out -p prmtop -c inpcrd -r 01_Min.rst -inf 01_Min.mdinfo *
>>> *> > At line 668 of file mdread1.F90 (unit = 5, file = '01_Min.in') *
>>> *> > Fortran runtime error: End of file *
>>> *> > linux-0bye nikolay/Tutorial# *
>>> *> > *
>>> *> > I also have attached mdread1.F90 file which contains FATAL ERROR
>>> messages *
>>> *> > in it. *
>>> *> > Please tell me how could I fix it. *
>>> *> > *
>>> *> > Kind regards, *
>>>
>>>
>>> *> > Nick*
>>> Dear Carlos,
>>>
>>> thanks for your advice, I have deleted these spaces
>>> but the same error message appears again...
>>> Is there a problem still in 01_Min.in file,
>>> that is, Amber can't see the &cntrl character in it?
>>>
>>> Kind regards,
>>> Nick
>>>
>>> 2015-11-30 14:39 GMT+03:00 Nikolay N. Kuzmich <nnkuzmich.gmail.com>:
>>>
>>>> Dear Bill, David and other Amber users,
>>>>
>>>> I enclose a copy of the 01_Min.in file.
>>>> How should it be formatted correctly?..
>>>> Also an extra blank line at the end mdread1.F90 file was added,
>>>> but it didn't help.
>>>> So what can be done next?..
>>>> I am a beginner at Amber and compiling, etc.
>>>> so hope for your empathy.
>>>>
>>>> Kind regards,
>>>> Nick
>>>>
>>>> 2015-11-27 11:28 GMT+03:00 Nikolay N. Kuzmich <nnkuzmich.gmail.com>:
>>>>
>>>>> Dear Amber users,
>>>>>
>>>>> When I launched minimization procedure in course of the alanine
>>>>> dipeptide tutorial
>>>>> I have received an error message:
>>>>>
>>>>> linux-0bye nikolay/Tutorial# $AMBERHOME/bin/sander -O -i 01_Min.in -o
>>>>> 01_Min.out -p prmtop -c inpcrd -r 01_Min.rst -inf 01_Min.mdinfo
>>>>> At line 668 of file mdread1.F90 (unit = 5, file = '01_Min.in')
>>>>> Fortran runtime error: End of file
>>>>> linux-0bye nikolay/Tutorial#
>>>>>
>>>>> I also have attached mdread1.F90 file which contains FATAL ERROR
>>>>> messages in it.
>>>>> Please tell me how could I fix it.
>>>>>
>>>>> Kind regards,
>>>>> Nick
>>>>>
>>>>> Nikolay Kuzmich, PhD
>>>>> Department of Drug Safety
>>>>> Research Institute of Influenza
>>>>> WHO National Influenza Centre of Russia
>>>>> 197376 Saint-Petersburg
>>>>> http://www.influenza.spb.ru/en/
>>>>> 15/17 Professor Popov St.
>>>>> Tel.: +78124991559
>>>>> Mobile: +79213491750
>>>>> e-mail: nikolay.kuzmich.influenza.spb.ru
>>>>> nnkuzmich.gmail.com
>>>>>
>>>>
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Received on Fri Dec 04 2015 - 01:30:04 PST
