Are the patches already included in the source code or necessary to be installed?


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You could use the following commands:

cd $NWCHEM_TOP/src
wget http://nwchemgit.github.io/images/Util_md_sockets.patch.gz
gzip -d Util_md_sockets.patch.gz
patch -p0 < Util_md_sockets.patch

You need to repeat the process for each patch.