AMBER Archive (2007)

Subject: Re: AMBER: errors in SHIFTS execution

From: Thomas Pochapsky (pochapsk_at_brandeis.edu)
Date: Mon Jul 30 2007 - 09:06:19 CDT

Also, this is the contents of "reduce.info"

sh: /tcpl1/tomp/nab-5.1.2/bin/reduce: No such file or directory

On Jul 29, 2007, at 11:44 AM, David A. Case wrote:

> On Sat, Jul 28, 2007, Tom Pochapsky wrote:
>
>> Hi, I have installed SHIFTS 4.2 as a subdirectory of NAB 5.1.2 on
>> Linux
>> Red Hat. NAB installed fine, and passed all tests.
>>
>> Make install for SHIFTS worked without obvious errors, but the last
>> lines of output from "make test" gave the following error messages:
>>
>> < 132d CYT 24 H3' -0.05 0.29 0.00 0.00 4.36 4.60
>> < 132d CYT 24 H2'1 -0.35 0.15 0.00 0.00 2.24 2.04
>> < 132d CYT 24 H2'2 -0.12 0.09 0.00 0.00 2.17 2.14
>> FAILED (possibly: see if diffs above look OK)
>> =====================================================
>> Running test for carbon/nitrogen shifts in a protein
>>
>> ../bin/shifts -qdb -refine 1acf
>> make[1]: *** [1acf_test] Segmentation fault
>> make[1]: Leaving directory `/amnt/tcpl1/tomp/nab-5.1.2/shifts-4.2/
>> test'
>> make: *** [test] Error 2
>
> What computer and OS are you using? Which parameters did you use
> in the
> configure script for nab?
>
>>
>> Also, when I attempted to run the bpti test, I get output with no
>> rings
>> found and the following "messages" file:
>>
>>> shifts will be computed for atoms matching ::H*
>>>
>>> Getting sequence from 132d.atom
>>>
>>>
>>> Getting coordinates from 132d.atom
>>>
>>> Got 0 coordinates using getxyz_from_pdb
>>>
>>> Reading observed shifts from 132d.obs
>
> This is odd, since "132d" is the name of files from the nucleic
> acid test
> case, not the bpti one. How did you "run the bpti test", and did
> it work
> when it was run from the "make test" script?
>
> My rough suspicion is that the "reduce" program (which is a
> relatively new
> addition to shifts, and has not probably been tested on as many
> platforms)
> may be failing for you. Take a look at the "reduce.info" file to
> see if there
> are any clues there.
>
>
> ...dac
>
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