You have "-c inpcrd" which says to use a file named inpcrd (default
name) for the starting coordinates.
Typically for minimization this is the file you created with
saveamberparm in leap. Note the 'prmtop' file is created at the same time.
Bill
On 12/1/15 1:27 AM, Nikolay N. Kuzmich wrote:
> 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 Tue Dec 01 2015 - 02:30:04 PST
