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<FONT FACE="Verdana, Helvetica, Arial"><SPAN STYLE='font-size:12.0px'>Thank you to those who helped me with yesterday’s question regarding the proper version of fftw. I now notice that the website has a new clear message.<BR>
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I am now working through the tutorials and have hit a second snag, in that my computer is not recognizing the commands “demo” or “pdb2gmx”. I have successfully configured and installed both fftw and gromacs. Upon installation, the program placed the /bin file (which contains pdb2gmx) inside of another directory, powerpc-apple-darwin7.6.0. I tried setting the path in two ways using the setenv command described in the online documentation, first as (in my case) /Users/jbozell/gromacs/bin, and then as /Users/jbozell/gromacs/ powerpc-apple-darwin7.6.0/bin. In both cases, when I moved to the directory containing the first demo, entering “demo” resulted in the reply “command not found”. I have also copied the bin file from its initial location into the gromacs file and reset the path as /Users/jbozell/gromacs/bin. Again, the command is not recognized. I get the same result from entering pdb2gmx.<BR>
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At present, my primary interest in using gromacs is to generate topology files for pdbs of small molecules that I prepare in ChemDraw and Chem3D. Gromacs was suggested as an excellent tool to carry out these transformations. <BR>
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Workstation info: Mac Powerbook G4, OS 10.3.6<BR>
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Thanks again for any direction.<BR>
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Best regards,<BR>
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Joe Bozell<BR>
Principal Scientist <BR>
National Renewable Energy Laboratory<BR>
Golden, CO<BR>
USA</SPAN></FONT>
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