Hi all and thanks to Tom and Erick for your reply. I tried this option: /lib/cpp -traditional and there are no more warning, on the contrary I have not clear that in the file ffambernb.itp the charge are 0.00 and also the mass, that I manually wrote, I mean: [ atomtypes ] ; name bond_type mass charge ptype sigma epsilon amber94_1 BR 0.0000 0.0000 A 0.00000e+00 0.00000e+00 amber94_2 C 0.00000 0.0000 A 3.39967e-01 3.59824e-01 amber94_3 CA 0.00000 0.0000 A 3.39967e-01 3.59824e-01
and I manually wrote only the masses, not the charges, Anyone knows if this could generate problems with MD? thanks in advance, Adriana > Hi Tom, > > I'm not sure if it works, but if you are using gcc you could try > setting this in your mdp file: > > cpp = "cpp -traditional-cpp" > > Or, -no-traditional-cpp - I never remember which flag is which... > > > Cheers, > > Erik > > On Apr 28, 2006, at 3:53 PM, Tomas Kubar wrote: > > > hi > > > > the file ffamber94bon.itp defines the parameters as macros. some of > > the macro names contain an asterisk character (*), e.g. > > #define proper_X_CT_N*_X 0.00000 0.00000 0.00000 > > 0.00000 0.00000 0.00000 > > this makes the preprocessor issue a warning (no whitespace after > > macro name) because a macro name is not allowed to contain this > > character. it looks like this might lead to wrong macro expansion > > in case this dihedral is contained in the molecule's topology. > > right now, I don't have an idea how to fix this... > > > > tom > > > > Adriana Pietropaolo wrote: > >> Dear gmx users, > >> I have some problems to use amber force field. > >> When I try to use grompp with a topology created with ffamber* (I > >> download each files from the gromacs home page) there are these > >> errors: > >> missing terminating ' character > >> ffamber94bon.itp:384:116: missing terminating ' character > >> ffamber94bon.itp:385:116: missing terminating ' character > >> ffamber94bon.itp:391:116: missing terminating ' character > >> ffamber94bon.itp:423:23: warning: ISO C requires whitespace after > >> the macro nameffamber94bon.itp:425:23: warning: ISO C requires > >> whitespace after the macro nameffamber94bon.itp:426:23: warning: > >> ISO C requires whitespace after the macro nameffamber94bon.itp: > >> 429:22: warning: ISO C requires whitespace after the macro > >> nameffamber94bon.itp:438:20: warning: ISO C requires whitespace > >> after the macro namecpp exit code: 256 > >> I found in the web some similar posts but I did not find any reply. > >> Would you suggest me some advice? > >> Thank you for your kind attention, > >> cheers, > >> Adriana > > _______________________________________________ > > 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 > > > > _______________________________________________ > 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 > -- _____________________________________________ Adriana Pietropaolo, PhD student, dipartimento di Chimica Fisica ed Inorganica, Facolta' di Chimica Industriale Universita' di Bologna WEB:www2.fci.unibo.it/~adriana Tel 051/6446992 FAX 051/2093690 _____________________________________________ _______________________________________________ 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
