Dear Charles,
I think that worked but now my AMBERHOME is set to amber16 directory, I can
use my commands in any folder. How can I use AmberTools18 files like parmed
and tleap without making pwd in to amber18 directory?
Regards,
On Wed, May 30, 2018 at 10:41 AM, Charles Lin <clin92.ucsd.edu> wrote:
> 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
>
--
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
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Received on Wed May 30 2018 - 01:00:03 PDT
