Re: [AMBER-Developers] Final push: AmberTools19 release candidate 3

From: David Case <>
Date: Sun, 21 Apr 2019 01:34:32 +0000

On Sat, Apr 20, 2019, Scott Brozell wrote:
>Here is one sequence of commands to get a dir for amber18 for
>candidate 3 testing:
>mkdir test
>chmod 700 test
>cd test
>git clone amber18
>cd amber18/
>git checkout amber18-with-patches
>cd ..
>gtar jxf ~/tmp/AmberTools19.19apr19.tar.bz2

Note that it is important to do the tar command *after* you have checked
out the amber18-with-patches branch, not before. When you do a
subsequent configure step, you should not be asked to apply any patches.
(If you *do* get a request to apply patches, something has gone wrong, and
continue from that point is not going to be helpful.)

>This last command emits:
>gtar: amber18/AmberTools/src/packmol_memgen/packmol_memgen/data/pdbs: Cannot open: File exists
>gtar: Exiting with failure status due to previous errors
>which is not a real issue since the exiting occurs after everything
>is untarred.

Above problem has been fixed by Stephan Schott; fix will be in the next
release candidate (if there is one). It will lead to one
test failure inovlving packmol_memgen, which you can ignore.

A further note: the pmemd you will have should be the same as the pmemd
in Amber18, with one exception, involving the location of the AmberNetcdf.F90
file. Please be attentive for any serial or parallel build errors for
pmemd. Try to see if any you find might also be present in the pristine
amber18-with-patches branch.


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Received on Sat Apr 20 2019 - 19:00:02 PDT
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