[gmx-users] g_protonate: Can't find ffgmx2 library files

[Sarath Chandra]

On Fri, Dec 10, 2010 at 12:16 PM, Jon Kapla <jon.kapla at mmk.su.se> wrote:

> Hi,
>
> Since I upgraded gromacs to > 4.5 I can't use g_protonate the way I'm used
> to. The error I get is that it can't find ffgmx2 library files in current
> dir or GMXLIB.    The problem, I guess, could possibly be that g_protonate
> has not been updated to the new forcefield structure in share/gromacs/top.
>

In Gromacs4.5.x the structure of the top directory has changed. The path for
.hdb file is in gmx2.ff and under the name aminoacids.hdb

Changing your GMXLIB would solve the problem...

for eg: /usr/local/gromacs/45x/share/gromacs/top

--

Sarath

>
> The documentation still says that a ffgmx2.hdb file should be used, but
> nothing about any changes in behaviour of g_protonate itself. It does not
> work to set GMXLIB to the topology dir of the old 4.0.7 install dir either
> since I then get an error about a missing residue datfile or something
> similar.
>
> I still can protonate using the old versions of protonate (4.07, 4.0.5)
> using a custom ffgmx2.hdb-file, but It would be nice to be able to use the
> tpr files directly (if I do this with new 4.5.x trajectories I get a version
> mismatch).
>
> Have I missed some major change of usage, or do you have any other
> suggestions to my problem?
>
> Regards
> Jon Kapla
>
>
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