[gmx-users] Error during PUMED installation for GROMACS-4.5.3

[bipin singh]

Hello,
I am getting following error while installing PLUMED for gromacs
Please suggest if someone has succesfully installed PLUMED on GROMACS-4.5.3.
The error is as below:
-----------------------------------------------------------------------------------------------
root at bipin-OptiPlex-330:/usr/local/gromacs# ./plumedpatch_gromacs_4.5.1.sh-patch
* I will try to patch PLUMED version 1.2.2 ...
-- Executing pre script
-- Setting up symlinks
ln: creating symbolic link `./src/kernel//metadyn.h': File exists
ln: creating symbolic link `./src/kernel//biasexchange.c': File exists
ln: creating symbolic link `./src/kernel//hills.c': File exists
ln: creating symbolic link `./src/kernel//metadyn.c': File exists
ln: creating symbolic link `./src/kernel//ptmetad.c': File exists
ln: creating symbolic link `./src/kernel//read_restraint.c': File exists
ln: creating symbolic link `./src/kernel//restraint_alfabeta.c': File exists
ln: creating symbolic link `./src/kernel//restraint_alpharmsd.c': File
exists
ln: creating symbolic link `./src/kernel//restraint_angle.c': File exists
ln: creating symbolic link `./src/kernel//restraint_antibetarmsd.c': File
exists
ln: creating symbolic link `./src/kernel//restraint.c': File exists
ln: creating symbolic link `./src/kernel//restraint_coord.c': File exists
ln: creating symbolic link `./src/kernel//restraint_dihcor.c': File exists
ln: creating symbolic link `./src/kernel//restraint_dipole.c': File exists
ln: creating symbolic link `./src/kernel//restraint_dist.c': File exists
ln: creating symbolic link `./src/kernel//restraint_elstpot.c': File exists
ln: creating symbolic link `./src/kernel//restraint_energy.c': File exists
ln: creating symbolic link `./src/kernel//restraint_hbonds.c': File exists
ln: creating symbolic link `./src/kernel//restraint_helix.c': File exists
ln: creating symbolic link `./src/kernel//restraint_mindist.c': File exists
ln: creating symbolic link `./src/kernel//restraint_parabetarmsd.c': File
exists
ln: creating symbolic link `./src/kernel//restraint_position.c': File exists
ln: creating symbolic link `./src/kernel//restraint_puckering.c': File
exists
ln: creating symbolic link `./src/kernel//restraint_rgyr.c': File exists
ln: creating symbolic link `./src/kernel//restraint_rmsdtor.c': File exists
ln: creating symbolic link `./src/kernel//restraint_spath.c': File exists
ln: creating symbolic link `./src/kernel//restraint_torsion.c': File exists
ln: creating symbolic link `./src/kernel//restraint_waterbridge.c': File
exists
ln: creating symbolic link `./src/kernel//restraint_zpath.c': File exists
ln: creating symbolic link `./src/kernel//testderivatives.c': File exists
-- Applying patches
patching file ./src/kernel/md.c
Hunk #1 succeeded at 86 with fuzz 3 (offset -1 lines).
Hunk #2 succeeded at 1514 with fuzz 3 (offset -2 lines).
Hunk #3 FAILED at 1928.
1 out of 3 hunks FAILED -- saving rejects to file ./src/kernel/md.c.rej
patching file ./src/kernel/mdrun.c
Hunk #1 succeeded at 55 with fuzz 3 (offset -1 lines).
Hunk #2 FAILED at 373.
Hunk #3 succeeded at 632 with fuzz 3 (offset -2 lines).
1 out of 3 hunks FAILED -- saving rejects to file ./src/kernel/mdrun.c.rej
patching file ./src/kernel/repl_ex.c
Hunk #1 succeeded at 51 with fuzz 3.
Hunk #2 FAILED at 84.
Hunk #3 FAILED at 154.
Hunk #4 succeeded at 214 with fuzz 3 (offset -1 lines).
Hunk #5 succeeded at 229 with fuzz 3 (offset -2 lines).
Hunk #6 succeeded at 523 with fuzz 3 (offset -3 lines).
Hunk #7 succeeded at 551 with fuzz 3 (offset -4 lines).
Hunk #8 FAILED at 585.
Hunk #9 FAILED at 638.
Hunk #10 FAILED at 679.
Hunk #11 succeeded at 771 with fuzz 3 (offset -5 lines).
5 out of 11 hunks FAILED -- saving rejects to file
./src/kernel/repl_ex.c.rej
patching file ./src/kernel/Makefile
Hunk #1 succeeded at 9 with fuzz 3 (offset -10 lines).
Hunk #2 FAILED at 138.
Hunk #3 FAILED at 160.
Hunk #4 FAILED at 362.
Hunk #5 FAILED at 379.
Hunk #6 succeeded at 522 with fuzz 3 (offset -11 lines).
Hunk #7 succeeded at 582 with fuzz 3 (offset -12 lines).
Hunk #8 succeeded at 605 with fuzz 3 (offset -13 lines).
4 out of 8 hunks FAILED -- saving rejects to file ./src/kernel/Makefile.rej
patching file ./src/kernel/repl_ex.h
Hunk #1 succeeded at 68 with fuzz 3 (offset -1 lines).
-- Executing post script
touch: cannot touch `./src/kernel//.deps/biasexchange.Po': No such file or
directory
touch: cannot touch `./src/kernel//.deps/hills.Po': No such file or
directory
touch: cannot touch `./src/kernel//.deps/metadyn.Po': No such file or
directory
touch: cannot touch `./src/kernel//.deps/ptmetad.Po': No such file or
directory
touch: cannot touch `./src/kernel//.deps/read_restraint.Po': No such file or
directory
touch: cannot touch `./src/kernel//.deps/restraint_alfabeta.Po': No such
file or directory
touch: cannot touch `./src/kernel//.deps/restraint_alpharmsd.Po': No such
file or directory
touch: cannot touch `./src/kernel//.deps/restraint_angle.Po': No such file
or directory
touch: cannot touch `./src/kernel//.deps/restraint_antibetarmsd.Po': No such
file or directory
touch: cannot touch `./src/kernel//.deps/restraint.Po': No such file or
directory
touch: cannot touch `./src/kernel//.deps/restraint_coord.Po': No such file
or directory
touch: cannot touch `./src/kernel//.deps/restraint_dihcor.Po': No such file
or directory
touch: cannot touch `./src/kernel//.deps/restraint_dipole.Po': No such file
or directory
touch: cannot touch `./src/kernel//.deps/restraint_dist.Po': No such file or
directory
touch: cannot touch `./src/kernel//.deps/restraint_elstpot.Po': No such file
or directory
touch: cannot touch `./src/kernel//.deps/restraint_energy.Po': No such file
or directory
touch: cannot touch `./src/kernel//.deps/restraint_hbonds.Po': No such file
or directory
touch: cannot touch `./src/kernel//.deps/restraint_helix.Po': No such file
or directory
touch: cannot touch `./src/kernel//.deps/restraint_mindist.Po': No such file
or directory
touch: cannot touch `./src/kernel//.deps/restraint_parabetarmsd.Po': No such
file or directory
touch: cannot touch `./src/kernel//.deps/restraint_position.Po': No such
file or directory
touch: cannot touch `./src/kernel//.deps/restraint_puckering.Po': No such
file or directory
touch: cannot touch `./src/kernel//.deps/restraint_rgyr.Po': No such file or
directory
touch: cannot touch `./src/kernel//.deps/restraint_rmsdtor.Po': No such file
or directory
touch: cannot touch `./src/kernel//.deps/restraint_spath.Po': No such file
or directory
touch: cannot touch `./src/kernel//.deps/restraint_torsion.Po': No such file
or directory
touch: cannot touch `./src/kernel//.deps/restraint_waterbridge.Po': No such
file or directory
touch: cannot touch `./src/kernel//.deps/restraint_zpath.Po': No such file
or directory
touch: cannot touch `./src/kernel//.deps/testderivatives.Po': No such file
or directory
touch: cannot touch `./src/kernel//.deps/*.Po': No such file or directory
- DONE!


-- 
*
---------------------------------
Thanks and regards
Bipin Singh
*
*
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