Hello,<br>I am getting following error while installing PLUMED for gromacs<br>Please suggest if someone has succesfully installed PLUMED on GROMACS-4.5.3.<br>The error is as below:<br>-----------------------------------------------------------------------------------------------<br>
root@bipin-OptiPlex-330:/usr/local/gromacs# ./<a href="http://plumedpatch_gromacs_4.5.1.sh">plumedpatch_gromacs_4.5.1.sh</a> -patch<br>* I will try to patch PLUMED version 1.2.2 ...<br>-- Executing pre script<br>-- Setting up symlinks<br>
ln: creating symbolic link `./src/kernel//metadyn.h': File exists<br>ln: creating symbolic link `./src/kernel//biasexchange.c': File exists<br>ln: creating symbolic link `./src/kernel//hills.c': File exists<br>
ln: creating symbolic link `./src/kernel//metadyn.c': File exists<br>ln: creating symbolic link `./src/kernel//ptmetad.c': File exists<br>ln: creating symbolic link `./src/kernel//read_restraint.c': File exists<br>
ln: creating symbolic link `./src/kernel//restraint_alfabeta.c': File exists<br>ln: creating symbolic link `./src/kernel//restraint_alpharmsd.c': File exists<br>ln: creating symbolic link `./src/kernel//restraint_angle.c': File exists<br>
ln: creating symbolic link `./src/kernel//restraint_antibetarmsd.c': File exists<br>ln: creating symbolic link `./src/kernel//restraint.c': File exists<br>ln: creating symbolic link `./src/kernel//restraint_coord.c': File exists<br>
ln: creating symbolic link `./src/kernel//restraint_dihcor.c': File exists<br>ln: creating symbolic link `./src/kernel//restraint_dipole.c': File exists<br>ln: creating symbolic link `./src/kernel//restraint_dist.c': File exists<br>
ln: creating symbolic link `./src/kernel//restraint_elstpot.c': File exists<br>ln: creating symbolic link `./src/kernel//restraint_energy.c': File exists<br>ln: creating symbolic link `./src/kernel//restraint_hbonds.c': File exists<br>
ln: creating symbolic link `./src/kernel//restraint_helix.c': File exists<br>ln: creating symbolic link `./src/kernel//restraint_mindist.c': File exists<br>ln: creating symbolic link `./src/kernel//restraint_parabetarmsd.c': File exists<br>
ln: creating symbolic link `./src/kernel//restraint_position.c': File exists<br>ln: creating symbolic link `./src/kernel//restraint_puckering.c': File exists<br>ln: creating symbolic link `./src/kernel//restraint_rgyr.c': File exists<br>
ln: creating symbolic link `./src/kernel//restraint_rmsdtor.c': File exists<br>ln: creating symbolic link `./src/kernel//restraint_spath.c': File exists<br>ln: creating symbolic link `./src/kernel//restraint_torsion.c': File exists<br>
ln: creating symbolic link `./src/kernel//restraint_waterbridge.c': File exists<br>ln: creating symbolic link `./src/kernel//restraint_zpath.c': File exists<br>ln: creating symbolic link `./src/kernel//testderivatives.c': File exists<br>
-- Applying patches<br>patching file ./src/kernel/md.c<br>Hunk #1 succeeded at 86 with fuzz 3 (offset -1 lines).<br>Hunk #2 succeeded at 1514 with fuzz 3 (offset -2 lines).<br>Hunk #3 FAILED at 1928.<br>1 out of 3 hunks FAILED -- saving rejects to file ./src/kernel/md.c.rej<br>
patching file ./src/kernel/mdrun.c<br>Hunk #1 succeeded at 55 with fuzz 3 (offset -1 lines).<br>Hunk #2 FAILED at 373.<br>Hunk #3 succeeded at 632 with fuzz 3 (offset -2 lines).<br>1 out of 3 hunks FAILED -- saving rejects to file ./src/kernel/mdrun.c.rej<br>
patching file ./src/kernel/repl_ex.c<br>Hunk #1 succeeded at 51 with fuzz 3.<br>Hunk #2 FAILED at 84.<br>Hunk #3 FAILED at 154.<br>Hunk #4 succeeded at 214 with fuzz 3 (offset -1 lines).<br>Hunk #5 succeeded at 229 with fuzz 3 (offset -2 lines).<br>
Hunk #6 succeeded at 523 with fuzz 3 (offset -3 lines).<br>Hunk #7 succeeded at 551 with fuzz 3 (offset -4 lines).<br>Hunk #8 FAILED at 585.<br>Hunk #9 FAILED at 638.<br>Hunk #10 FAILED at 679.<br>Hunk #11 succeeded at 771 with fuzz 3 (offset -5 lines).<br>
5 out of 11 hunks FAILED -- saving rejects to file ./src/kernel/repl_ex.c.rej<br>patching file ./src/kernel/Makefile<br>Hunk #1 succeeded at 9 with fuzz 3 (offset -10 lines).<br>Hunk #2 FAILED at 138.<br>Hunk #3 FAILED at 160.<br>
Hunk #4 FAILED at 362.<br>Hunk #5 FAILED at 379.<br>Hunk #6 succeeded at 522 with fuzz 3 (offset -11 lines).<br>Hunk #7 succeeded at 582 with fuzz 3 (offset -12 lines).<br>Hunk #8 succeeded at 605 with fuzz 3 (offset -13 lines).<br>
4 out of 8 hunks FAILED -- saving rejects to file ./src/kernel/Makefile.rej<br>patching file ./src/kernel/repl_ex.h<br>Hunk #1 succeeded at 68 with fuzz 3 (offset -1 lines).<br>-- Executing post script<br>touch: cannot touch `./src/kernel//.deps/biasexchange.Po': No such file or directory<br>
touch: cannot touch `./src/kernel//.deps/hills.Po': No such file or directory<br>touch: cannot touch `./src/kernel//.deps/metadyn.Po': No such file or directory<br>touch: cannot touch `./src/kernel//.deps/ptmetad.Po': No such file or directory<br>
touch: cannot touch `./src/kernel//.deps/read_restraint.Po': No such file or directory<br>touch: cannot touch `./src/kernel//.deps/restraint_alfabeta.Po': No such file or directory<br>touch: cannot touch `./src/kernel//.deps/restraint_alpharmsd.Po': No such file or directory<br>
touch: cannot touch `./src/kernel//.deps/restraint_angle.Po': No such file or directory<br>touch: cannot touch `./src/kernel//.deps/restraint_antibetarmsd.Po': No such file or directory<br>touch: cannot touch `./src/kernel//.deps/restraint.Po': No such file or directory<br>
touch: cannot touch `./src/kernel//.deps/restraint_coord.Po': No such file or directory<br>touch: cannot touch `./src/kernel//.deps/restraint_dihcor.Po': No such file or directory<br>touch: cannot touch `./src/kernel//.deps/restraint_dipole.Po': No such file or directory<br>
touch: cannot touch `./src/kernel//.deps/restraint_dist.Po': No such file or directory<br>touch: cannot touch `./src/kernel//.deps/restraint_elstpot.Po': No such file or directory<br>touch: cannot touch `./src/kernel//.deps/restraint_energy.Po': No such file or directory<br>
touch: cannot touch `./src/kernel//.deps/restraint_hbonds.Po': No such file or directory<br>touch: cannot touch `./src/kernel//.deps/restraint_helix.Po': No such file or directory<br>touch: cannot touch `./src/kernel//.deps/restraint_mindist.Po': No such file or directory<br>
touch: cannot touch `./src/kernel//.deps/restraint_parabetarmsd.Po': No such file or directory<br>touch: cannot touch `./src/kernel//.deps/restraint_position.Po': No such file or directory<br>touch: cannot touch `./src/kernel//.deps/restraint_puckering.Po': No such file or directory<br>
touch: cannot touch `./src/kernel//.deps/restraint_rgyr.Po': No such file or directory<br>touch: cannot touch `./src/kernel//.deps/restraint_rmsdtor.Po': No such file or directory<br>touch: cannot touch `./src/kernel//.deps/restraint_spath.Po': No such file or directory<br>
touch: cannot touch `./src/kernel//.deps/restraint_torsion.Po': No such file or directory<br>touch: cannot touch `./src/kernel//.deps/restraint_waterbridge.Po': No such file or directory<br>touch: cannot touch `./src/kernel//.deps/restraint_zpath.Po': No such file or directory<br>
touch: cannot touch `./src/kernel//.deps/testderivatives.Po': No such file or directory<br>touch: cannot touch `./src/kernel//.deps/*.Po': No such file or directory<br>- DONE!<br><br clear="all"><br>-- <br><font color="#3333ff"><i><font face="arial, helvetica, sans-serif"><div>
---------------------------------<br>Thanks and regards<br></div><div><span style="font-family: arial; font-style: normal;"><i><font face="arial, helvetica, sans-serif">Bipin Singh</font></i></span></div></font></i></font><div>
<font color="#3333ff" face="arial, helvetica, sans-serif"><i><br></i></font></div><br>