[gmx-users] problem in executing genbox command
devicerandom at gmail.com
Sun Nov 7 13:57:59 CET 2010
On 06/11/10 07:46, Mark Abraham wrote:
> On 6/11/2010 4:02 PM, bharat gupta wrote:
>> Hi all ,
>> Whenever i am running the genbox command I am getting the following
>> error :-
>> genbox -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top
>> :-) G R O M A C S (-:
>> Segmentation fault (core dumped)
> The most likely scenario is some shared library is not available when it
> should be. That means the environment in which you ran the above command
> is different from the one in which GROMACS was built. That means
> most/all GROMACS commands will fail. A possibility is that there's a bug
> in GROMACS, but I doubt it. Do other GROMACS commands, or other genbox
> runs work?
A missing library should show explicitly as such, not as a segfault. I
suspect some compilation glitch. What compiler did you use? On what system?
A good idea would be to run the command through gdb.
>> Can anybody tell me whats the reason for such an error ...
>> Ph.D. Candidate
>> Room No. : 7202A, 2nd Floor
>> Biomolecular Engineering Laboratory
>> Division of Chemical Engineering and Polymer Science
>> Pusan National University
>> Busan -609735
>> South Korea
>> Lab phone no. - +82-51-510-3680, +82-51-583-8343
>> Mobile no. - 010-5818-3680
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Massimo Sandal, Ph.D.
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