[gmx-users] how to get pdb2gmx to use an arbitrarily located forcefield.ff directory?

[francesco oteri]

Hi Chris,
I don't know if thngs changed in gromacs 4.6.x, but I succesfully did what
you are triying to do setting the two variable GMXLIB and GMXDATA at the
same time.

Francesco


2013/3/5 Christopher Neale <chris.neale at mail.utoronto.ca>

> Hello,
>
> I have downloaded the charmm36.ff directory and would like to use it with
> pdb2gmx. Everything works fine if I put it in the current directory or the
> share/gromacs/top directory of the binary that I am using. However, I'd
> like to be able to put the charmm36.ff directory in an arbitrary place.
>
> I tried setting GMXLIB, no luck. I also tried setting GMXDATA and also,
> separately, creating a directory structure share/gromacs/top/charm36ff and
> then setting GMXDATA to share/ (which seems absurdly convoluted, but is
> implied that it should work by the description of GMXDATA here
> http://www.gromacs.org/Documentation/Terminology/Environment_Variablesand the text at the output of pdb2gmx:
>
> Fatal error:
> Could not find force field 'charmm36' in current directory, install tree
> or GMXDATA path.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> I can get around this by making a link in the current directory and then
> using sed to change the directory structure in the resulting .top file,
> after which I can remove the link in the .top file.
>
> Thank you for any advice,
> Chris.
>
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-- 
Cordiali saluti, Dr.Oteri Francesco