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
> _______________________________________________
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> 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
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Received on Tue Feb 13 2018 - 06:00:03 PST
