On Mon, Jun 17, 2013 at 12:44 PM, Hunter Brown <bassoongoon.earthlink.net>wrote:
> Okay thank you. I have successfully compiled and installed amber WITHOUT
> the patches. How can I get the patches after the installation? Do I just
> run update amber?
>
> Correct me if I am wrong: I need to (1) look for the patch files (2)
> delete the dos endings (3) run update amber.
>
> I really appreciate your help.
>
I'm preparing a patch now that will 'fix' update_amber to work with Cygwin.
This should be available shortly, and I'll respond with updated
instructions.
All the best,
Jason
>
> -Hunter
>
> -----Original Message-----
> >From: Daniel Roe <daniel.r.roe.gmail.com>
> >Sent: Jun 17, 2013 10:10 AM
> >To: Hunter Brown <bassoongoon.earthlink.net>, AMBER Mailing List <
> amber.ambermd.org>
> >Subject: Re: [AMBER] Difficulty compiling amber12/ambertools13
> >
> >Hi,
> >
> >This is actually an issue with dos line endings in the patch file
> >confusing 'patch' under cygwin. If you remove the dos line endings
> >from the patch, updating should occur successfully:
> >
> >$> cd $AMBERHOME
> >$> ./configure -cygwin gnu
> >...
> >Applying AmberTools 13/update.4
> >PatchingError: .patches/AmberTools13_Unapplied_Patches/update.4 failed
> >to apply. No changes made from this patch
> >Automatic patching failed! Check the errors before re-configuring
> >$> dos2unix.exe .patches/AmberTools13_Unapplied_Patches/update.4
> >dos2unix: converting file
> >.patches/AmberTools13_Unapplied_Patches/update.4 to Unix format ...
> >$> ./configure -cygwin gnu
> >...
> >
> >A fix to update_amber is also in the works to correct this.
> >
> >-Dan
> >
> >On Fri, Jun 14, 2013 at 4:41 PM, Hunter Brown <bassoongoon.earthlink.net>
> wrote:
> >> Hello, I am having difficulty compiling amber12 and ambertools 13. I am
> a windows user, so I am working via Cygwin.
> >>
> >> When I try to apply patches I get this message:
> >>
> >>
> >>
> >> PatchingError: .patches/AmberTools13_Unapplied_Patches/update.4 failed
> to apply. No changes made from this patch
> >> Automatic patching failed! Check the errors before re-configuring
> >>
> >>
> >>
> >>
> >> When I try to skip the patches using './configure cygwin' I get this
> message:
> >>
> >>
> >>
> >>
> >>
> >> NOT updating your tree and continuing anyway.
> >> Could not find the X11 libraries; you may need to edit config.h
> >> to set the XHOME and XLIBS variables.
> >> Searching for python2... Found python2.7: /usr/bin/python2.7
> >> Error: Architecture/compiler 'cygwin' is not supported!
> >> Type './configure -help' for options.
> >> Configure failed due to the errors above!
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> I have tried using './configure gnu -cygwin' as well. The patches still
> fail to apply. If I try to skip the patches with './configure gnu -cygwin'
> I get this message (by the way, the single quotes are to make the commands
> I enter stand out from the rest of my text. I did not actually put single
> quotes into my Cygwin bash) :
> >>
> >>
> >>
> >>
> >> NOT updating your tree and continuing anyway.
> >> Error: unknown compiler: gnu
> >> Type './configure -help' for options.
> >> Configure failed due to the errors above!
> >>
> >>
> >>
> >>
> >>
> >>
> >> If somebody could help me get that sorted out I would really appreciate
> it. I need to learn Amber/Ambertools so that I can start running
> simulations. Because I have had difficulty configuring/compiling Amber, I
> cannot even reach the stage where I can begin learning how to use it; its
> frustrating!
> >>
> >>
> >>
> >>
> >>
> >> Anyways, thanks for reading and I hope that someone can be of
> assistance to me.
> >>
> >>
> >> -Hunter
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> >--
> >-------------------------
> >Daniel R. Roe, PhD
> >Department of Medicinal Chemistry
> >University of Utah
> >30 South 2000 East, Room 201
> >Salt Lake City, UT 84112-5820
> >http://home.chpc.utah.edu/~cheatham/
> >(801) 587-9652
> >(801) 585-9119 (Fax)
> >
> >_______________________________________________
> >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
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Jun 17 2013 - 10:00:03 PDT
