Hi, Thanks everybody by the comments. There was a error in the include files of the topology: The itp file generated by pdb2gmx program was localized in a different folder that where we were running to the grompp program.
Mario El mar, 08-05-2007 a las 02:05 +0100, TJ Piggot escribió: > Hi, > > With regards to the versions you are correct, ffamber_v3.3.1 is for use > with Gromacs 3.3.1. As for the error i would suggest you do what Mark says > and make sure all your inclusions are correct. If you still can't find the > problem then you need to post some of your .top file so we can have a look > at it > > Tom > > --On 08 May 2007 10:53 +1000 Mark Abraham <[EMAIL PROTECTED]> wrote: > > > root wrote: > >> Dear GROMACS user: > >> > >> Erik and Tom thanks by the comments, too. Sorry, I read the FAQ pages of > >> http://folding.stanford.edu and now I understand your comments. > >> We tried with cpp = /lib/cpp -traditional in the mdp file. The warning > >> desapears, but the error messages is similar. > >> (Fatal error: > >>>>> Atoms in the .top are not numbered consecutively from 1 > >>>>> > >>>>> ------------------------------------------------------- > >>>>> > >>>>> We tested the dick.top file, and we verified that the atoms > >>>> are numbered > >>>>> consecutively from 1 to 758.) > > > > Have you inspected the #included files as well? The way cpp works, any > > file #included is literally dropped into its parent file, so if you had > > something wrong in such an #inclusion you'd need to fix that. > > > > Mark > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before posting! > > 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 > > > > ---------------------- > TJ Piggot > [EMAIL PROTECTED] > University of Bristol, UK. > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > 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 gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
