Thank you for your response.
I have checked the min2.out file and the thing that I noticed was that the
file is incomplete when compared with the similar file from the tutorial.
Attached is min2.out file.
Please help.
*Akinyemi A. Omoniyi*
Faculty Member,
Department of Human Anatomy,
Faculty of Basic Medical Sciences,
College of Medical Sciences,
Ahmadu Bello University, Zaria, Nigeria.
E-mail: aaomoniyi.abu.edu.ng
Contact: +2347038862108
On Sat, Jun 5, 2021 at 6:29 PM David A Case <david.case.rutgers.edu> wrote:
> On Sat, Jun 05, 2021, Akinyemi Omoniyi wrote:
> >
> >I was running minimization following the tutorial available at
> >https://ambermd.org/tutorials/basic/tutorial1/section5.php. Stage 1
> >minimization (Holding the solute fixed) running successfully without any
> >error but the stage 2 minimization gives the error below.
> >
> >sander -O -i min2.in -o min2.out -p lassa_ion.prmtop -c min1.ncrst -r
> >min2.ncrst
> >
> >Program received signal SIGSEGV: Segmentation fault - invalid memory
> >reference.
>
> Look in the min2.out file: is there any hint there about what went wrong?
>
> >cd $AMBERHOME; make test.serial.cuda and get
> >make: *** No rule to make target 'test.serial.cuda'. Stop.
>
> The target is 'test.cuda.serial'
>
> >(cd AmberTools/test && make test.cuda.serial)
> >make[1]: Entering directory
> >'/home/akinyemi/Downloads/Amber20/amber20/AmberTools/test'
> >Makefile:2: /config.h: No such file or directory
> ^^^^^^^^^^
>
> This indiates that your $AMBERHOME variable is not set correctly. Make
> sure
> you have sourced the amber.sh file in
> /home/akinyemi/Downloads/Amber20/amber20. Type "echo $AMBERHOME" to check
> things.
>
> (But these cuda problems should be unrelated to the sander error reported
> above.)
>
> ....dac
>
>
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- application/octet-stream attachment: min2.out
Received on Sat Jun 05 2021 - 15:30:02 PDT
