It is self-contained, but both use the same cmake scripts. They depend on the user passing the PMEMD_ONLY flag. If you provide information on what you have tried, we can help you further.
Stephan Schott Verdugo
Biochemist
Computational Biophysical Chemistry
Institut für Bio- und Geowissenschaften / Bioinformatik (IBG-4)
Forschungszentrum Jülich GmbH
Wilhelm-Johnen-Straße, 52425 Jülich
Germany
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Forschungszentrum Jülich GmbH
52425 Jülich
Sitz der Gesellschaft: Jülich
Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
Dr. Stephanie Bauer (stellvertretende Vorsitzende),
Prof. Dr. Ir. Pieter Jansens, Prof. Dr. Laurens Kuipers
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El mié, 13 may 2026 a la(s) 9:58 p.m., Weatherby,Gerard via AMBER (amber.ambermd.org<mailto:amber.ambermd.org>) escribió:
I don’t understand. The website says:
Note:There is a change from older versions of Amber: the pmemd26.tar.bz2 file is self-contained, and does not require AmberTools code to be compiled and run. Many users can use the conda package to run AmberTools on local machines, and compile pmemd26 on a high-performance machine suitable for large calculations.
If pmend24.tar.bz2 is self contained, why doesn’t pmemd26_src/AmberTools have all the directories reference in pmend26_src/cmake/*cmake?
From: Stephan Schott <s.schott-verdugo.fz-juelich.de<mailto:s.schott-verdugo.fz-juelich.de>>
Date: Wednesday, May 13, 2026 at 12:41 PM
To: Weatherby,Gerard <gweatherby.uchc.edu<mailto:gweatherby.uchc.edu>>, AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
Subject: Re: [AMBER] pmemd26 vs ambertools26
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That looks like either you are mixing pmemd and ambertools folder structures, or you are not passing the PMEMD_ONLY option to cmake. Check the included run_cmake script and modify from there. Let us know if this was not the case.
Stephan Schott Verdugo
Biochemist
Computational Biophysical Chemistry
Institut für Bio- und Geowissenschaften / Bioinformatik (IBG-4)
Forschungszentrum Jülich GmbH
Wilhelm-Johnen-Straße, 52425 Jülich
Germany
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Forschungszentrum Jülich GmbH
52425 Jülich
Sitz der Gesellschaft: Jülich
Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
Dr. Stephanie Bauer (stellvertretende Vorsitzende),
Prof. Dr. Ir. Pieter Jansens, Prof. Dr. Laurens Kuipers
---------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------
El mié, 13 may 2026 a la(s) 4:52 p.m., Weatherby,Gerard via AMBER (amber.ambermd.org<mailto:amber.ambermd.org><mailto:amber.ambermd.org<mailto:amber.ambermd.org>>) escribió:
The way I’m reading the install directions we compile either pmemd26_src or ambertools26. When I try to compile the pmem26_src I’m getting missing directory errors.
add_subdirectory given source "gbnsr6" which is not an existing directory.
add_subdirectory given source "cifparse" which is not an existing
add_subdirectory given source "addles" which is not an existing directory.
add_subdirectory given source "sander" which is not an existing directory.
add_subdirectory given source "nmr_aux" which is not an existing directory.
add_subdirectory given source "nmode" which is not an existing directory.
add_subdirectory given source "antechamber" which is not an existing
add_subdirectory given source "sqm" which is not an existing directory.
add_subdirectory given source "sebomd" which is not an existing directory.
add_subdirectory given source "ndiff-2.00" which is not an existing
add_subdirectory given source "gem.pmemd" which is not an existing
add_subdirectory given source "xray" which is not an existing directory.
add_subdirectory given source "cpptraj" which is not an existing directory.
add_subdirectory given source "ambpdb" which is not an existing directory.
add_subdirectory given source "pbsa" which is not an existing directory.
add_subdirectory given source "sff" which is not an existing directory.
add_subdirectory given source "rism" which is not an existing directory.
add_subdirectory given source "mdgx" which is not an existing directory.
add_subdirectory given source "xtalutil" which is not an existing
add_subdirectory given source "saxs" which is not an existing directory.
add_subdirectory given source "mm_pbsa" which is not an existing directory.
add_subdirectory given source "paramfit" which is not an existing
add_subdirectory given source "FEW" which is not an existing directory.
add_subdirectory given source "cphstats" which is not an existing
add_subdirectory given source "quick" which is not an existing directory.
add_subdirectory given source "cew" which is not an existing directory.
add_subdirectory given source "nfe-umbrella-slice" which is not an existing
add_subdirectory given source "leap" which is not an existing directory.
add_subdirectory given source "parmed" which is not an existing directory.
add_subdirectory given source "mmpbsa_py" which is not an existing
add_subdirectory given source "pymsmt" which is not an existing directory.
add_subdirectory given source "pysander" which is not an existing
add_subdirectory given source "pytraj" which is not an existing directory.
add_subdirectory given source "pdb4amber" which is not an existing
add_subdirectory given source "packmol_memgen" which is not an existing
add_subdirectory given source "PyPE_RESP" which is not an existing
add_subdirectory given source "proprep" which is not an existing directory.
add_subdirectory given source "rismtools" which is not an existing
add_subdirectory given source "moft" which is not an existing directory.
add_subdirectory given source "nabc" which is not an existing directory.
add_subdirectory given source "fe-toolkit" which is not an existing
add_subdirectory given source "examples" which is not an existing
add_subdirectory given source "benchmarks" which is not an existing
add_subdirectory given source "dat" which is not an existing directory.
These all seem to existing in the ambertools tarball. Are we supposed to extract both tarballs?
-----------------------------------
GERARD WEATHERBY
Application Architect
NMRhub
nmrhub.org<
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Forschungszentrum Jülich GmbH
52425 Jülich
Sitz der Gesellschaft: Jülich
Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
Dr. Stephanie Bauer (stellv. Vorsitzende),
Prof. Dr. Ir. Pieter Jansens, Prof. Dr. Laurens Kuipers
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
Forschungszentrum Jülich GmbH
52425 Jülich
Sitz der Gesellschaft: Jülich
Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
Dr. Stephanie Bauer (stellv. Vorsitzende),
Prof. Dr. Ir. Pieter Jansens, Prof. Dr. Laurens Kuipers
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AMBER mailing list
AMBER.ambermd.org<mailto:
AMBER.ambermd.org>
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Forschungszentrum Jülich GmbH
52425 Jülich
Sitz der Gesellschaft: Jülich
Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
Dr. Stephanie Bauer (stellv. Vorsitzende),
Prof. Dr. Ir. Pieter Jansens, Prof. Dr. Laurens Kuipers
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
Forschungszentrum Jülich GmbH
52425 Jülich
Sitz der Gesellschaft: Jülich
Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
Dr. Stephanie Bauer (stellv. Vorsitzende),
Prof. Dr. Ir. Pieter Jansens, Prof. Dr. Laurens Kuipers
------------------------------------------------------------------------------------------------
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Received on Fri May 15 2026 - 07:30:03 PDT
