[gmx-users] gromacs3.3 problem after installation

[Erik Lindahl]

Hi,

We won't be able to help without details, details, details:

* What type hardware do you have?
* Which operation system, and which version?
* How did you install Gromacs? Did you compile yourself or use a  
package?
* If you compiled it, which compiler and version (cc --version or  
something) are you using?
* Did you get any strange output/warnings when running configure?
* Were there any errors/warnings when building?
* Did you have any earlier Gromacs version working?
* Did you uninstall that before running "make install" (in case you  
installed from source)
* Do any other Gromacs commands work (e.g. "luck" that just echoes  
one of the "cool quotes")

Cheers,

Erik


On Oct 12, 2005, at 7:35 PM, Wang Zhun wrote:

> Hi,
> I've installed version 3.3 but failed to get it work.
> Eg: pdb2gmx is in my path but cannot be found, and  segmentation  
> fault will occur if it's carried out.
> I don't know what's the problem.
>
>
> [wzh at hewei wzh]$ pdb2gmx -h
> tmpstrtrp[i]tmpstrtrp[i]tmpstrtra and K.  
> Nemototmpstrtrtmpstrtrtmpstrtrtmpstrtrtmpstrtrtmpstrtrtmpstrtrtmpstrtr 
> p[i]tmpstrtrp[i]t of range  
> (135930989)----------------------------------------------------------- 
> -
> No filetype (null)
> d argument rint help info for option (null)Segmentation fault
> [wzh at hewei wzh]$ whereis pdb2gmx
> pdb2gmx:
> [wzh at hewei wzh]$ ls /usr/local/gromacs/bin/pdb2gmx
> /usr/local/gromacs/bin/pdb2gmx*
> [wzh at hewei wzh]$ echo $PATH
> /usr/local/bin:/bin:/usr/bin:/usr/X11R6/bin:/usr/games:/usr/X11R6/ 
> bin:/usr/games:/usr/X11R6/bin:/usr/games:/usr/X11R6/bin:/usr/ 
> games:.:/usr/X11R6/bin:/usr/games:/usr/local/gromacs/bin:/home/wzh/ 
> biolinux/autodock/bin:/home/wzh/bin
> [wzh at hewei wzh]$  /usr/local/gromacs/bin/pdb2gmx
> tmpstrtrp[i]tmpstrtrp[i]tmpstrtra and K.  
> Nemototmpstrtrtmpstrtrtmpstrtrtmpstrtrtmpstrtrtmpstrtrtmpstrtrtmpstrtr 
> p[i]tmpstrtrp[i]t of range  
> (135930989)----------------------------------------------------------- 
> -
> No filetype (null)
> d argument rint help info for option (null)Segmentation fault
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-----------------------------------------------------------
Erik Lindahl  <lindahl at sbc.su.se>
Assistant Professor, Stockholm Bioinformatics Center
Stockholm University, SE 106 91 Stockholm
Phone: +46 8 5537 8564     Fax: +46 8 5537 8214