Thanks for the answer Mr. Jason.
I've removed all the comments after the \ and there are no more inpcrd
files error. but now appears "Segmentation fault (core dumped)" after
sander execution, and i only get
mdin, mdinfo, min1.o, and min1.nc as the output file. i've attached my
command revision and the output files. Is there another mistake from my
command?
Thank you
Best regards,
Christian Yongky
Faculty of Pharmacy
University of Indonesia
> You can't have comments (or even spaces) after the \ at the end of every
> line (called a continuation). The forward slash "cancels" the special
> meaning of the character following it. The character whose special meaning
> you want to cancel is the line break (which means "end the command and
> start a new one).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>> On Mar 23, 2015, at 2:47 AM, christian.yongky.ui.ac.id wrote:
>>
>> Dear Amber users,
>>
>> My name is Christian Yongky,
>> I'm an undergraduate student at University of Indonesia.
>> Currently I'm studying Amber for molecular dynamic simulation,
>> particulary
>> in Tutorial A15 which is a simulation of room temperature ionic liquid.
>> I'm using Amber12.
>> I have following the tutorial and there are no problems until
>> minimization
>> with sander on step 6, it said that my inpcrd file is missing or
>> unreadable but i've checked the file and it's exist. I also attached the
>> files from the tleap one step before, the inpcrd file and my shellscript
>> for minimization.
>> Is there something wrong with my work? or there is something else wrong?
>> Any help or suggestions will be highly appreciated.
>>
>> Thank you
>>
>> Best Regards,
>> Christian Yongky
>> Faculty of Pharmacy
>> University of Indonesia
>> <ionicbox.inpcrd>
>> <leap.log>
>> <runmin.sh>
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>
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- application/octet-stream attachment: mdin
- application/x-object attachment: min1.o
- application/x-netcdf attachment: min1.nc
- application/octet-stream attachment: mdinfo
- application/x-shellscript attachment: runmin.sh
Received on Mon Mar 23 2015 - 03:30:02 PDT
