Configuring the .itp files etc initially is a bit tricksy without knowing what you're doing, the short not-very-helpful answer is "read the manual". There's a whole chapter (5?) on forcefield files and their formats. It's entirely possible to set it all up so that pdb2gmx does in fact work, but to do this you need to edit the forcefield files in the main gromacs folder for these things (add your lipid.itp and dppc.itp, add "#include" for each of these to your forcefield of choice). Anyways: I'd guess it was complaining initially because #include files were in the wrong order in your .top, and then subsequently because you removed the reference to lipid.itp (which you need). Unless someone can be of more help, I suggest you just tinker.
--- toma0052 <[EMAIL PROTECTED]> wrote: > Hi, > I am new to Gromacs, and I am working with > lipid bilayer simulations. > I am attempting to just run an energy minimization > on a lipid bilayer so I > can get a better feel for the program. I have taken > the files dppc128.pdb, > dppc.itp, lipid.itp and example2.itp from Peter > Tieleman's website. > Because I could not use teh pdb2gmx command, I > started with the editconf > command and then the genbox command, both of which > seemed to run > successfully. Then, I tried to do the preprocessing > with the grompp > command, but I received the error; Fatal Error: > Found a second defaults > directive, file "lipid.itp". When I removed > lipid.itp from the topology > file, I received the error; Fatal Error: Atomtype > 'LC3' not found! As I > said before, I am new to Gromacs, and I am not sure > how to get around this > problem. Do I need to put the dppc.itp and lipid.itp > file together into > one? Any help would be appreciated. > > Thanks, > Mike Tomasini > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the > list. Use the > www interface or send it to > [EMAIL PROTECTED] > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
