Thank you, now it works..I was trying to be the smart kid :)
Elisa
On Tue, Feb 13, 2018 at 2:46 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> The only time I've seen this happen is when you have a version of
> Amber that has been somehow modified from outside the normal patching
> process, e.g. local changes have been made or you have copied from a
> GIT version somehow. I think your best bet in such situations is to
> start from a clean source tree (i.e. the unmodified Amber and
> AmberTools tarballs).
>
> -Dan
>
> On Tue, Feb 13, 2018 at 4:27 AM, Elisa Pieri <elisa.pieri90.gmail.com>
> wrote:
> > Hello,
> >
> > I'm reinstalling Amber16 on my machine, but I get this error in the
> > updating:
> >
> > 10:20:49 $ ./configure gnu
> > Checking for updates...
> > Checking for available patches online. This may take a few seconds...
> >
> > Available AmberTools 17 patches:
> >
> > No patches available
> >
> > Available Amber 16 patches:
> >
> > update.9 (modifies pmemd)
> > Description:
> > a) Add the &pmd, &bbmd and &stsm module to PMEMD
> > b) Fix the bug when running with NPT ensemble
> > c) Fix the bug which leads to wrong work in &smd
> >
> > update.10 (modifies pmemd, pmemd.cuda)
> > Description:
> > fixes a vulnerability that would have allowed LJ 12-6-4 to be
> > applied with incompatible options.
> >
> > update.11 (modifies pmemd)
> > Description:
> > fixes gamd log output for multiple gamd simulations.
> >
> > update.12 (modifies pmemd.cuda, &, pmemd.cuda.MPI)
> > Description:
> > Fixes nstep and dt being broken for oscillating electric fields.
> >
> >
> > There are patches available. Do you want to apply them now? [y/N]
> > (Recommended Y)
> > y
> > Preparing to apply updates... please wait.
> > No new updates available for AmberTools 17
> > Applying Amber 16/update.9
> > PatchingError: .patches/Amber16_Unapplied_Patches/update.9 failed to
> apply.
> > No changes made from this patch
> > Automatic patching failed! Check the errors before re-configuring
> >
> > This is the result of "patch -p0 -N --dry-run <
> > .patches/Amber16_Unapplied_Patches/update.9":
> >
> > checking file src/pmemd/src/Makefile
> > Hunk #1 FAILED at 55.
> > 1 out of 1 hunk FAILED
> > checking file src/pmemd/src/f90depends
> > Hunk #1 FAILED at 482.
> > Hunk #2 FAILED at 494.
> > Hunk #3 FAILED at 986.
> > 3 out of 3 hunks FAILED
> > checking file src/pmemd/src/gb_force.F90
> > Hunk #1 FAILED at 339.
> > 1 out of 1 hunk FAILED
> > checking file src/pmemd/src/nfe_abmd.F90
> > checking file src/pmemd/src/nfe_bbmd.F90
> > checking file src/pmemd/src/nfe_colvar.F90
> > checking file src/pmemd/src/nfe_lib.F90
> > checking file src/pmemd/src/nfe_pmd.F90
> > checking file src/pmemd/src/nfe_setup.F90
> > checking file src/pmemd/src/nfe_smd.F90
> > checking file src/pmemd/src/nfe_stsm.F90
> > checking file src/pmemd/src/pme_force.F90
> > Hunk #1 FAILED at 468.
> > Hunk #2 FAILED at 1487.
> > 2 out of 2 hunks FAILED
> > checking file src/pmemd/src/runmd.F90
> > Hunk #1 FAILED at 83.
> > Hunk #2 FAILED at 2945.
> > Hunk #3 FAILED at 2960.
> > 3 out of 3 hunks FAILED
> >
> > What is going on?
> >
> > Thank you,
> > Elisa
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Feb 13 2018 - 07:00:03 PST
