Uhh, it'd probably be preferable to run it with AmberTools16 as I think your Amber installation might be missing some patches which might have some broken functionality for some features. Basically by putting the src folder in your amber 18 folder, its expecting amber 18 source files, so when its trying to apply diffs through the patcher, its not finding the files it needs to patch against, so you're not actually receiving any amber 16 patches on top of the basically tarball.
Charlie
________________________________
From: senal dinuka <senal.ichemc.edu.lk>
Sent: Wednesday, May 30, 2018 12:30:50 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Automatic patching failed!
Thank Charles Lin,
Would it be ok to proceed with my current installation for mpi and cuda
support?
Regards,
On Wed, May 30, 2018 at 9:54 AM, Charles Lin <clin92.ucsd.edu> wrote:
> 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.
>
>
> -Charlie
> ________________________________
> From: senal dinuka <senal.ichemc.edu.lk>
> 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)
> Description:
> 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)
> 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
> AmberTools18*
>
> Regards,
> --
> D L Senal Dinuka
> Grad.Chem., A.I.Chem.C.
> Research Assistant
> College of Chemical Sciences
> Institute of Chemistry Ceylon
> Rajagiriya
> Sri Lanka
> +94 77 627 4678
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
D L Senal Dinuka
Grad.Chem., A.I.Chem.C.
Research Assistant
College of Chemical Sciences
Institute of Chemistry Ceylon
Rajagiriya
Sri Lanka
+94 77 627 4678
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue May 29 2018 - 22:30:02 PDT
