[gmx-users] using the correct .rtp files

Christoph Freudenberger christoph.freudenberger at chemie.uni-ulm.de
Fri Jun 20 08:58:01 CEST 2003

David L. Bostick wrote:
> One more suggestion,..
> IN a worst case scenario, you can always set the includes in the mdp file
> to the explicit path ...
> i.e. instead of
> include   = -I$GMXDATA/top
> do
> include   = -I/usr/local/my/crazy/long/path/top
> to make grompp search only that directory and your current working
> directory.  At least then you wouldn't have to keep copies of your topology
> in your current working directory..  If that doesn't work, I'd say you have
> a much deeper problem than path variables..

The solution you suggest will only work with grompp, but not with
tools like pdb2gmx who also use files from /top.

You only report problems with pdb2gmx looking in the wrong directory.
Is grompp also looking up the same dir?

I suppose there must be something wrong with the path variables.
Doublecheck $GMXDATA and possible interference with .[shell]rc and
or GMXRC (perhaps you have set $GMXDATA before sourcing GMXRC or something
like that)

Or it is a bug (or feature ;-) of pdb2gmx. Maybe one of the developers
could comment on where it looksa for the top's.

Christoph Freudenberger
Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785

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