Thank you, Francesco, for the assistance. However, I still can not get it to work (see below). Can you please specify exactly what you have done and perhaps show a listing of the directory structure?
My command was: pdb2gmx -f protein.pdb -ff charmm36 I tried this in a number of ways, all eventually failed: neither GMXLIB or GMXDATA set: Error: "Could not find force field 'charmm36' in current directory, install tree or GMXDATA path." # define GMXDATA export GMXLIB="" export GMXDATA=~/gromacs/CHARMM36/share Error: "Could not find force field 'charmm36' in current directory, install tree or GMXDATA path." # define GMXLIB: export GMXLIB=~/gromacs/CHARMM36/share/gromacs/top export GMXDATA="" the charmm36 ff is found, but after selecting a water model, I get: Error: "Library file residuetypes.dat not found in current dir nor in your GMXLIB path." # define both: export GMXDATA=~/gromacs/CHARMM36/share export GMXLIB=~/gromacs/CHARMM36/share/gromacs/top the charmm36 ff is found, but after selecting a water model, I get: Error: "Library file residuetypes.dat not found in current dir nor in your GMXLIB path." # set GMXLIB to the regular installation: export GMXDATA=~/gromacs/CHARMM36/share export GMXLIB=/usr/local/gromacs-4.5.5/share/gromacs/top/ Error: "Could not find force field 'charmm36' in current directory, install tree or GMXDATA path." # the reverse of the idea above: export GMXDATA=/usr/local/gromacs-4.5.5/share export GMXLIB=~/gromacs/CHARMM36/share/gromacs/top Error: "Library file residuetypes.dat not found in current dir nor in your GMXLIB path." Here is a listing of the artificial directory structure that I created to try to get this to work: [nealec@pegasus check]$ ls ~/gromacs/CHARMM36/ share [nealec@pegasus check]$ ls ~/gromacs/CHARMM36/share/ gromacs [nealec@pegasus check]$ ls ~/gromacs/CHARMM36/share/gromacs/ top [nealec@pegasus check]$ ls ~/gromacs/CHARMM36/share/gromacs/top/ charmm36.ff [nealec@pegasus check]$ ls ~/gromacs/CHARMM36/share/gromacs/top/charmm36.ff/ aminoacids.arn aminoacids.n.tdb aminoacids.vsd dna.arn dna.n.tdb ffnabonded.itp forcefield.doc ions.itp popc.itp rna.hdb rna.rtp tip3p.itp watermodels.dat aminoacids.c.tdb aminoacids.r2b atomtypes.atp dna.c.tdb dna.rtp ffnanonbonded.itp forcefield.itp lipids.hdb rna.arn rna.n.tdb spce.itp tip4p.itp aminoacids.hdb aminoacids.rtp cmap.itp dna.hdb ffbonded.itp ffnonbonded.itp gb.itp lipids.rtp rna.c.tdb rna.r2b spc.itp tips3p.itp Thank you, Chris. -- original message -- 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 <[hidden email]> > 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. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
