[gmx-users] fatal error in grompp

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Nov 21 12:03:16 CET 2006

Hi Argyrios,

It means that grompp expects a file aminoacids.dat, which is a library
file, but can't find it in your current directory and it can't find it
in directories which grompp searches by default. Additionally, grompp
gives you a suggestion to solve it, mentioning that you can set a
variable, GMXLIB, containing directories to search for library files.

Now I'm really tempted to stop the reply here. The error message was
perfectly clear. You need to locate aminoacids.dat which should be in
the subdirectory /share/gromacs/top of the directory where you have
gromacs installed. The GMXLIB environment variable should point to
that directory.


On 11/21/06, Argyrios Karatrantos <axk47 at psu.edu> wrote:
>  HI
>  i am doing a grompp command, and i am getting the following fatal error:
>  Library file aminoacids.dat not found in current dir nor in default
> directories. (you can set the directories to search with the GMXLIB path
> variable)
> what that means?
> thank you in advance
>  Argyris Karatrantos
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Tsjerk A. Wassenaar, Ph.D.
NMR, Utrecht University,
Padualaan 8,
3584 CH Utrecht, the Netherlands
P: +31-30-2539931
F: +31-30-2537623

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