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

[Jon Kapla]

This still does not work.

I source the gromacs tree with GMXRC first. Then I set the GMXLIB to the 
share/gromacs/top/. I have a custom ffgmx2.hdb (which works fine in 
4.0.7) in my working directory to protonate united atom trajectories of 
lipid bilayer simulations. So this is what I have:

$ echo $GMXLIB
/Volumes/gravensteiner/install/gromacs4.5.2/share/gromacs/top/
$ which g_protonate
/Volumes/gravensteiner/install/gromacs4.5.2/bin/g_protonate

And the error is exactly this:

Program g_protonate, VERSION 4.5.2
Source code file: futil.c, line: 891

Fatal error:
Library file ffgmx2 not found in current dir nor in your GMXLIB path.

And it stops, doing nothing. I get the same with version 4.5.3.

I'm open to more suggestions! :)

Regards
Jon



On 12/10/2010 12:52 PM, Sarath Chandra wrote:
>
>
> On Fri, Dec 10, 2010 at 12:41 PM, Jon Kapla <jon.kapla at mmk.su.se 
> <mailto:jon.kapla at mmk.su.se>> wrote:
>
>     Thank you for the answer
>
>     Does this mean that if I want to use a custom .hdb-file in the
>     working directory it should be named aminoacids.hdb?
>     Shouldn't GMXLIB be set when sourcing bin/GMXRC by the way? It
>     seems to be empty after sourcing on both my machines.
>     Not a big problem though.
>
>
> You dont have to rename anything. You can either add the following 
> line to your .bashrc (if using bash)
>
> export GMXLIB="/usr/local/gromacs/45x/share/gromacs/top"
>
>
> or run the  same command on your terminal
>
>
> Best Wishes,
>
> Sarath
>
>     Regards
>     Jon
>
>
>
>
>
>     On 12/10/2010 12:30 PM, Sarath Chandra wrote:
>
>
>         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
>
>

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