Toppar change log

All files in the toppar subdirectory that are included in the final
release (eg. files in toppar_jul16/toppar) will be maintained in the
Michigan GIT.  The procedure will allow for the files to be maintained
locally at UMB and then uploaded into the git repository prior to new
releases of CHARMM.  This will assure consistency with the UM Git.
Information on performing the process is in the MacKerell lab wiki.

http://mackerell.umaryland.edu/pmwiki/pmwiki.php?n=Main.CharmmGitRepositoryAtUMich

ls -R toppar/* > toppar_files_umb.list' from the local /raid/alex/param/toppar_jul18

and

'ls -R toppar/* > toppar_files_git.list' from the local /raid/alex/charmm/code/charmm_git

!Diff to identify files to add to or rename in Michigan Git

diff toppar_files_umb.list ../../charmm/code/charmm_git/toppar_files_git.list
< toppar_all36_lipid_ether.str
168,169c167
< toppar_all36_prot_c36_d_aminoacids.str
< toppar_all36_prot_c36m_d_aminoacids.str
---
> toppar_all36_prot_d_aminoacids.str

> toppar_all36_prot_mod_d_aminoacids.str

#commands to perform in /raid/alex/charmm/code/charmm_git PRIOR to copying "cp -r ../../../param/toppar_jul18/toppar ."

#make sure everything is up to date prior to making changes.
git pull

git mv toppar/stream/prot/toppar_all36_prot_d_aminoacids.str toppar/stream/prot/toppar_all36_prot_c36_d_aminoacids.str
git mv toppar/stream/prot/toppar_all36_prot_mod_d_aminoacids.str toppar/stream/prot/toppar_all36_prot_c36m_d_aminoacids.str

cp -r ../../../param/toppar_jul18/toppar .

#add new file
git add toppar/stream/lipid/toppar_all36_lipid_ether.str
#add updated files 
git add toppar/drude/drude_toppar_2017_7.tgz
git add toppar/par_all36_cgenff.prm
git add toppar/stream/lipid/toppar_all36_lipid_list.str
git add toppar/stream/lipid/toppar_all36_lipid_model.str
git add toppar/stream/na/toppar_all36_na_reactive_rna.str
git add toppar/stream/na/toppar_all36_na_modifications.str
git add toppar/stream/prot/toppar_all36_prot_c36_d_aminoacids.str
git add toppar/stream/prot/toppar_all36_prot_modify_res.str
git add toppar/top_all36_prot.rtf
git add toppar/toppar_all.history

git status

git commit -a -m "2017 to 2018 charmm toppar updates.  see toppar_all.history for details"

git push origin master

###
