Re: [AMBER] Automatic patching failed!

From: Charles Lin <>
Date: Wed, 30 May 2018 04:24:18 +0000

AmberTools 18 patches and Amber 16 patches are probably incompatible. The patcher searches for updates for Amber 18 not Amber 16. I'd suggest getting AmberTools17 or AmberTools 16 with your Amber 16, and having a separate installation with AmberTools 18. So you'll have 2 folders amber16 (containing AT17/AT16 + A16) and amber18 (containing AT18). Tools from AmberTools 18 will be compatible for running your simulations using Amber16.

From: senal dinuka <>
Sent: Wednesday, May 30, 2018 12:10:54 AM
To: AMBER Mailing List
Subject: [AMBER] Automatic patching failed!

Dear Amber users,
I was able to compile Amber16 engine along with AmberTools18 and run all
the test without any issue. But there was an error reported when I try to
update at the configuration step. I was able to proceed without applying
the relevant patch. I have amended the reported the error below. Please can
you clarify on this. Is this due to any missing packages or an issue with
the source code?

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

Available AmberTools 18 patches:

No patches available

Available Amber 18 patches:

update.1 (modifies pmemd)
Released on May 21, 2018 (written by Vinicius Wilian D. Cruzeiro)
    Adds an error message when users run REMD and the box sizes are not the
same across all replicas.

There are patches available. Do you want to apply them now? [y/N]
(Recommended Y)
Preparing to apply updates... please wait.
No new updates available for AmberTools 18
Applying Amber 18/update.1
PatchingError: .patches/Amber18_Unapplied_Patches/update.1 failed to apply.
No changes made from this patch
Automatic patching failed! Check the errors before re-configuring

*P.S My AMBERHOME is defined as ../Amber18 due to first extraction of

D L Senal Dinuka
Grad.Chem., A.I.Chem.C.
Research Assistant
College of Chemical Sciences
Institute of Chemistry Ceylon
Sri Lanka
+94 77 627 4678
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Received on Tue May 29 2018 - 21:30:03 PDT
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