<br><br><div class="gmail_quote">On Fri, Dec 10, 2010 at 12:16 PM, Jon Kapla <span dir="ltr"><<a href="mailto:jon.kapla@mmk.su.se">jon.kapla@mmk.su.se</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi,<br>
<br>
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.<br>
</blockquote><div><br>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<br><br>Changing your GMXLIB would solve the problem...<br><br>for eg: /usr/local/gromacs/45x/share/gromacs/top<br>
<br>--<br><br>Sarath <br></div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
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.<br>
<br>
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).<br>
<br>
Have I missed some major change of usage, or do you have any other suggestions to my problem?<br>
<br>
Regards<br>
Jon Kapla<br><font color="#888888">
<br>
<br>
-- <br>
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