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

[Justin A. Lemkul]

Jon Kapla wrote:
>   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! :)
> 

This is a known bug:

http://bugzilla.gromacs.org/show_bug.cgi?id=589

-Justin

> 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
>>
>>
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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