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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Received on Sat Jun 05 2021 - 09:30:02 PDT
