AMBER Archive (2007)

Subject: Re: AMBER: errors in SHIFTS execution

From: Thomas Pochapsky (pochapsk_at_brandeis.edu)
Date: Mon Jul 30 2007 - 08:49:47 CDT

Hi, Dave, we are running RedHat Enterprise Linux v. 4 with 3.06 GHz
dual Xeon processors. I did only the basic install for NAB (make
install and make test), no flags set. The "make test" for Shifts
did find the 6pti.pdb file and calculated ring current shifts correctly.

The only part of the "make test" output that seemed to indicate a
problem was the section I sent in the first message.

Thanks,
Tom P.
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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