[AMBER] Question on Updating AMBER

From: Gulsevin,Alican <agulsevin.ufl.edu>
Date: Tue, 19 Aug 2014 08:18:58 -0400


I was running some calculations involving a) PMEMD, b) Quasi-Harmonic
Analysis and AMBER14 stopped working, giving GpuBuffer errors first for
the PMEMD calculations, only killing the Quasi-Harmonic analysis jobs
without giving any warnings. After this, I thought updating AMBER might
be a good idea, for some of the newer patches contain fixes for cpptraj
and MMPBSA.py I am using, which could help.

When I try to update amber by ./update_amber --update command, I get
the following answer:

Preparing to apply updates... please wait.
Applying AmberTools 14/update.1
instance: .patches/AmberTools14_Unapplied_Patches/update.1 failed to
apply. No changes made from this patch

./update_amber --check-updates result in:

Checking for available patches online. This may take a few seconds...

Available AmberTools 14 patches:

update.1.bz2 (modifies No information available)
update.2 (modifies cpptraj, ParmEd, makeANG_RST, tleap, reduce, and,
update.3 (modifies ParmEd)
update.4 (modifies ParmEd, MMPBSA.py, tleap)
update.5 (modifies PBSA)
update.6 (modifies cpptraj)
update.7 (modifies paramfit, chamber)
update.8 (modifies AmberTools)
update.9 (modifies cpptraj)
update.10 (modifies netcdf)

which is followed by the description of the packages. Therefore, it is
not a server problem since I can check what is available on the server.

When I use ./update_amber --download-patches, all patches are
downloaded to the machine, so the problem apparently isn't with the
downloading part. I don't know how to overcome this, I still can't
update the program. Any help is appreciated.

Alican Gulsevin

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Received on Tue Aug 19 2014 - 05:30:04 PDT
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