Re: [AMBER] AMBER11 Installation on FEDORA 15

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Wed, 1 Jun 2011 00:14:07 -0400

Hi,

This is due to io.c being patched twice. Replace
$AMBERHOME/AmberTools/src/ptraj/io.c with the attached io.c, that
should fix it.

-Dan

On Tue, May 31, 2011 at 10:35 PM, Vivek Shankar Bharadwaj
<vbharadw.mymail.mines.edu> wrote:
> Hi dac,
>
> Thanks for the patch. I used the patch on the unpatched version of files.
>
> I get a new error now,
>
> a - wallclock.o
> ranlib arpack.a
> mv arpack.a /home/common/packages/amber11/lib
> make[2]: Leaving directory
> `/home/common/packages/amber11/AmberTools/src/arpack'
> gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ    -o main.o
> main.c
> gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ    -o rdparm.o
> rdparm.c
> gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ    -o dispatch.o
> dispatch.c
> gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ    -o help.o
> help.c
> gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ    -o utility.o
> utility.c
> gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ    -o second.o
> second.c
> gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ    -o io.o io.c
> io.c:782:5: error: conflicting types for ‘gzipFileSize’
> io.c:681:15: note: previous definition of ‘gzipFileSize’ was here
> io.c:814:5: error: conflicting types for ‘bzip2FileSize’
> io.c:728:15: note: previous definition of ‘bzip2FileSize’ was here
> io.c:840:5: error: conflicting types for ‘zipFileSize’
> io.c:755:15: note: previous definition of ‘zipFileSize’ was here
> make[1]: *** [io.o] Error 1
> make[1]: Leaving directory
> `/home/common/packages/amber11/AmberTools/src/ptraj'
> make: *** [serial] Error 2
>
> What could this be due to?
>
> Please Advice.
>
> Vivek
>
> On Mon, May 30, 2011 at 7:43 PM, case <case.biomaps.rutgers.edu> wrote:
>
>> On Mon, May 30, 2011, Vivek Shankar Bharadwaj wrote:
>> >
>> >          escf = escf + pm6_correction()
>> >                                      1
>> > Error: Function 'pm6_correction' at (1) has no IMPLICIT type
>>
>> OK: my bad.  The sqm routines that ship with AmberTools1.5 are actually
>> those
>> that were present in Amber11, not our most recent ones.
>>
>> You can try the attached patch (fingers crossed; use the files before you
>> applied the previous patch I posted).  But I'm hoping Andy or someone
>> familier
>> with sqm will vet this to see if it both makes sense, and is consistent
>> with
>> current code.
>>
>> Thanks for the report....dac
>>
>>
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>>
>>
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Received on Tue May 31 2011 - 21:30:02 PDT
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