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.
-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)
>
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>http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Jun 17 2013 - 10:00:02 PDT
