[gmx-users] www site is temporarily down
Hi all, There was a power outage which affected the www.gromacs.org server. The system is being fixed at the moment and therefore unreachable. We expect it to be online soon though. Cheers, Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] mpi run in Gromacs
Hi, I am a Phd student studying polymer membranes. I have installed Gromacs version 4.5.2 on our department cluster and attempted to run a simulations on a DPPC bilayer membranes taken from the tielleman website. I have set the system up in an NPT ensemble using a semi-isotropic pressure coupling. The simulation seems to run perfect in serial however I am having problems to run the simulation in parallel. I understand that this version of Gromacs uses threading to parallelise the system. I wanted to know whether it is possible to run this using openmpi and if not how do i use this thread base parallelisation. Many Thanks Selina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] water residence time on a certain group of ligand
Dear gromacs users, I want to calculate water molecules residence time on a certain groups of a ligand. I found in gromacs exercises how to do it: https://extras.csc.fi/chem/courses/gmx2004/exercises/index.html To get water residence time I need: 1) Obtain hbac.xvg, using this command: g_hbond -contact -n index -ac -r 0.6 -b 200 2) Integrate with g_analyze S0 and S1 (I am not quite sure S1 or S0). I used the command: g_hbond -contact -b 100 -nomerge -r 0.35 -f traj-prod315k.xtc -s prod.tpr -n index.ndx But I can not get the correct number of contacts with this command, because the output is : Back Off! I just backed up hbnum.xvg to ./#hbnum.xvg.4# Average number of contacts per timeframe 0.000 out of 612 possible -Is that mean that there is a zero contacts within a certain distance? I do not know is it does make sense to integrate So and S1 after using the command: g_hbond -contact -b 100 -nomerge -r 0.35 -f traj-prod315k.xtc -s prod.tpr -n index.ndx, because the program produce hbac.xvg file, but writes that no contacts were found. Please could you advice me on this? best, Olga -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] mpi run in Gromacs
Selina Nawaz skrev 2011-03-02 11.54: Hi, I am a Phd student studying polymer membranes. I have installed Gromacs version 4.5.2 on our department cluster and attempted to run a simulations on a DPPC bilayer membranes taken from the tielleman website. I have set the system up in an NPT ensemble using a semi-isotropic pressure coupling. The simulation seems to run perfect in serial however I am having problems to run the simulation in parallel. I understand that this version of Gromacs uses threading to parallelise the system. I wanted to know whether it is possible to run this using openmpi and if not how do i use this thread base parallelisation. Many Thanks Selina Hi, It's slightly different than you think. Gromacs uses a thread based MPI implementation for communications between cores on the same machine. If you compile without threads it would use e.g. OpenMPI instead of threads as far as I know. Note that it will still use OpenMPI (or equivalent) for inter-node communication. Cheers, -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Polarizable halide (Iodide)
On 2011-03-02 09.44, Mikhail Stukan wrote: David, What should not be working in the current version? Do you mean that any polarizable model (water for example) can run on a single processor only? I am currently using the model by Roux et al. for NaCl solution in SWM4-NDP model and everything seems to be working fine. I also had some problems with the collapsing of the system which seems to be solved by setting explicitly all pair interactions in [nonbond_param] statement (I had a feeling that mixing rule did not work for some reason). The results are very reasonable. Does it mean that I am doing something completely wrong? I have an open issue on this: http://redmine.gromacs.org/issues/713 maybe you can download the test files (based on the same model) that I put there and check them. Let's continue the discussion in the redmine forum. Many thanks in advance, Mikhail On 2011-03-01 22.06, Abhijeet Joshi wrote: Hi all, I am trying implement polarizable model for halides suggested by Roux group. I am not able to equilibrate such system. In present gromacs versions this runs on 1 processor (core) only. System: Sodium Iodide in water I am using following topology file for iodide. Anybody has any clue what might be happening? Question 2: I am having trouble finding implementation details for thole_polarization. How would that appear in topology file? ; ; Topology file for iodide polarizable [ moleculetype ] ; molnamenrexcl I1 [ atoms ] ; idat typeres nr residu nameat namecg nrcharge 1 II 1 SICI11 3.733085 2 IS1 SISI1-4.733085 [ polarization ] ; See notes above.alpha (nm^3) 121 0.007439 [ exclusions ] ; iatom excluded from interaction with i 12 21 #ifdef POSRES ; Restrain the oxygen... [ position_restraints ] ; iatom typefxfyfz 11100100100 #endif Your help will be greatly appreciated Thanks ~ Abhijeet -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Particle type 'B' in topology file?
Hi all, I have performed a simulation where for an atomtype, I accidentally put 'B' instead of 'A' which stands for 'atom'. The manual doesn't mention any 'B''s for particle type, (it mentions A,S,V and D). I have then corrected this (replaced B with A) and obtained a totally different configuration. I now wonder what have I used as particle type for the particle I have defined as type 'B'? What does B as particle type stand for? Atomtypes section of my topology file: [ atomtypes ] ;name masscharge ptype V(c6) W(c12) X 1 0.000 A1.0 1.0 Y 1 0.000 B1.0 1.0 Thanks, Cahit -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] mpi run in Gromacs
On 2/03/2011 11:37 PM, Erik Marklund wrote: Selina Nawaz skrev 2011-03-02 11.54: Hi, I am a Phd student studying polymer membranes. I have installed Gromacs version 4.5.2 on our department cluster and attempted to run a simulations on a DPPC bilayer membranes taken from the tielleman website. I have set the system up in an NPT ensemble using a semi-isotropic pressure coupling. The simulation seems to run perfect in serial however I am having problems to run the simulation in parallel. You're going to have to be much more specific if you want useful help. I understand that this version of Gromacs uses threading to parallelise the system. I wanted to know whether it is possible to run this using openmpi and if not how do i use this thread base parallelisation. Many Thanks Selina Hi, It's slightly different than you think. Gromacs uses a thread based MPI implementation for communications between cores on the same machine. If you compile without threads it would use e.g. OpenMPI instead of threads as far as I know. Note that it will still use OpenMPI (or equivalent) for inter-node communication. Not in 4.5.x. You can configure with MPI or threads (the default) or neither. The two cannot co-exist. Threading is only useful if a network is not involved. OpenMPI will do approximately the same via shared-memory as you can get from threading in the cases where it is useful. The OP should consult the GROMACS webpage for MPI installation instructions. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] oplsaa galactose
Hi, I am trying to simulate hexopyronase using OPLS-AA forcefield using parameters from the paper: An improved OPLS?AA force field for carbohydrates, 2002 by Gunsteren. The set of torsional angle parameters in the paper are given in Kcal/mol, but because I am using OPLS-AA I would need to convert the functions into RB-types, right? Is there a way to convert these functions to RB-types? Or do I convert them from Kcal/mol to KJ/mol? Thanks. Nisha P Quoting nishap.pa...@utoronto.ca: Thanks Justin! Quoting Justin A. Lemkul jalem...@vt.edu: nishap.pa...@utoronto.ca wrote: Hello, I am trying to simulate hexopyronase using OPLS-AA forcefield using parameters from the paper: An improved OPLS?AA force field for carbohydrates, 2002 by Gunsteren. I was looking through the ffoplsaabon.itp file and there are some dihedral parameters for hexopyronase. I am not sure what the comment below means. Below are extra dihedrals for some special organic molecules. ; Since the atom types are identical to other dihedrals you have to specify ; them explicitly with a define if you happen to simulate this type of molecule. How would I mention it in my rtp file? I don't understand ' specify them explicitly with a define' This is my .rtp for Galactose See examples in aminoacids.rtp, e.g. ARG. -Justin [ GLA ] [ atoms ] Oopls_180 -0.400 1 C1 opls_1950.365 2 H1opls_1960.100 2 O1opls_154 -0.683 2 HO1 opls_1550.418 2 C2 opls_1580.205 3 H2opls_1760.060 3 O2opls_154 -0.683 3 HO2 opls_1550.418 3 C3 opls_1580.205 4 H3opls_1760.060 4 O3opls_154 -0.683 4 HO3 opls_1550.418 4 C4 opls_1580.205 5 H4opls_1760.060 5 O4opls_154 -0.683 5 HO4 opls_1550.418 5 C5 opls_1830.170 6 H5opls_1850.030 6 C6opls_1570.145 7 H61 opls_1760.060 7 H62 opls_1760.060 7 O6opls_154 -0.683 7 HO6 opls_1550.418 7 [ bonds ] OC1 C1 H1 C1 O1 O1 HO1 C1 C2 C2 H2 C2 O2 O2 HO2 C2 C3 C3 H3 C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 O4 HO4 C4 C5 C5 C6 C5 O C6 H61 C6 H62 C6 O6 O6 HO6 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: adding ff parameter of modified residue to charmm ff
Hi, I followed the tutorial - http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field for updating the Charmm FF for my modified residue .. I added the residues to the .rtp file , then I added the new atom types in .atp file , The compound has some linkage with serine and glycine ... I want to know how and where shall I add the linkage parameters and the parameters (in bits) given below (The parameter file of the compound looks like this ) .. BONDS ! !V(bond) = Kb(b - b0)**2 ! !Kb: kcal/mole/A**2 !b0: A ! !atom type Kb b0 CA1 CA2 305.00 1.3750 ! CA2 CA3 305.00 1.3750 ! CA3 CA4 305.00 1.3750 ! HPc CA1 340.000 1.08 ! HPc CA2 340.000 1.08 ! HPc CA3 340.000 1.08 ! HPc CA4 340.000 1.08 ! ANGLES ! !V(angle) = Ktheta(Theta - Theta0)**2 ! !V(Urey-Bradley) = Kub(S - S0)**2 ! !Ktheta: kcal/mole/rad**2 !Theta0: degrees !Kub: kcal/mole/A**2 (Urey-Bradley) !S0: A ! !atom types KthetaTheta0 Kub S0 ! NR2c CP2c NR1c 130.00114.00 ! CP2c NR2c CP1c 130.00106.00 ! CP2c NR1c CP1c 130.00107.90 ! NR2c CP1c CP1c 130.00108.30 ! NR2c CP1c CE1c 45.80129.50 ! NR1c CP1c OcH42.00126.00 ! NR1c CP1c CP1c 130.00103.00 ! !Connection to the ser fragment !-- CT2 CT1 CP2c52.000 108. ! ALLOW ALI PEP POL ARO HB CT1 CP2c 50.000 109.5000 ! ALLOW PEP NH1 CT1 CP2c 50.000 107. ! ALLOW PEP POL ARO ALI NR2C CP2C CT1 40.00125.00 ! !Connection to the gly fragment !-- NR1C CT2 C 50.000 107. NR1c CT2 HB 48.000 108. CP2C NR1C CT2 36.00129.00 CP1C NR1C CT2 32.00123.40 ! DIHEDRALS ! !V(dihedral) = Kchi(1 + cos(n(chi) - delta)) ! !Kchi: kcal/mole !n: multiplicity !delta: degrees ! !atom types Kchin delta ! CP2C NR2C CP1C CP1C14. 2 180.00 ! CP2C NR1C CP1C CP1C14. 2 180.00 ! NR2C CP2C NR1C CP1C14. 2 180.00 ! NR2C CP1C CP1C NR1C 4. 2 180.00 ! NR1C CP2C NR2C CP1C 4. 2 180.00 ! CA1 CA2 CA3 CA4 3.1000 2 180.00 ! !barrier CA-CB CP1C CP1C CE1C HA1C 6.84 2 180.00 ! CP1C CP1C CE1C CA1 6.84 2 180.00 ! NR2C CP1C CE1C HA1C 6.84 2 180.00 ! NR2C CP1C CE1C CA1 6.84 2 180.00 ! ! !barrier CB-CG2 CP1C CE1C CA1 CA2 1.4 2 180.00 ! HA1C CE1C CA1 CA2 1.4 2 180.00 ! ! CP2C NR1C CP1C OCH 14.002 180.00 ! NR2C CP2C NR1C CT2 14.002 180.00 ! NR2C CP1C CP1C OCH 14.002 180.00 ! CP1C NR1C CP2C CT1 14.002 180.00 ! OCH CP1C NR1C CT2 14.002 180.00 ! CP1C NR2C CP2C CT1 14.002 180.00 ! CP1C CP1C NR1C CT2 14.002 180.00 ! CT1 CP2C NR1C CT2 14.002 180.00 ! ! ! Linking the chromophore and the glycine fragment OCCT2 NR1C 0. 1 0.00 ! NH1 CCT2 NR1c 0.6000 1 0.00 ! CP2C NR1C CT2 HB 0.032 3 0.00 ! CP2c NR1c CT2 C 0.032 3 0.00 ! CP1c NR1c CT2 HB 0.032 3 180.00 ! CP1c NR1c CT2 C 0.032 3 180.00 ! ! ! Linking the chromophore and the serine fragment CNH1 CT1 CP2C 0.2000 1 180.00 ! HNH1 CT1 CP2C 0. 1 0.00 ! NR2C CP2C CT1 HB 0.105 3 180.00 ! NR2C CP2C CT1 NH10.105 3 180.00 ! NR2C CP2C CT1 CT20.105 3 180.00 ! NR1C CP2C CT1 HB 0.105 3 0.00 ! IMPROPER ! !V(improper) = Kpsi(psi - psi0)**2 ! !Kpsi: kcal/mole/rad**2 !psi0: degrees !note that the second column of numbers (0) is ignored ! !atom types Kpsi psi0 ! CP2C NR2C NR1C CT1 0.5 0 0.00 CP2C NR1C NR2C CT1 0.5 0 0.00 ! CP1C NR1C CP1C OCH 0.5 0 0.00 CP1C CP1C NR1C OCH 0.5 0 0.00 ! NR1C CP1C CP2C CT2 0.45 0 0.00 NR1C CP2C CP1C CT2 0.45 0 0.00 ! CP1C NR2C CP1C CE1C 220.0 0 0.00 CP1C CP1C NR2C CE1C 220.0 0 0.00 ! !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] ! !epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) !Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j ! !atom ignoredepsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 ! !CAc5.00 -0.07 1.992400 ! ALLOW ARO !! benzene (JES) CA15.00 -0.07 1.992400 ! ALLOW ARO CA25.00 -0.07 1.992400 ! ALLOW ARO CA35.00 -0.07 1.992400 ! ALLOW ARO CA45.00 -0.07 1.992400 ! ALLOW ARO CE1c 0.00 -0.068000 2.09 ! ! for propene, yin/adm jr., 12/95 CP1c 0.00 -0.05 1.80 ! ALLOW ARO ! adm jr., 10/23/91, imidazole solvation and sublimation CP2c 0.00 -0.05 1.80 ! ALLOW ARO ! adm jr., 10/23/91, imidazole solvation and sublimation CT3c
[gmx-users] Error during PUMED installation for GROMACS-4.5.3
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@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
