Hi all, I've recently managed to reproduce the bug with x2top 4.x hanging at "atom 0". The halt occurred when I was trying to generate a topology with the "-pbc yes" option (which is the default used unless you specify otherwise) using a structure file containing no information on the periodic box. As soon as I added the box info, x2top 4.0.4 did successfully generate a topology for me.
I'm using x2top for periodic molecules (just forgot to add the box string this one time), so I didn't bother actually trying to turn off PBC, but I strongly suspect that this is the actual source of the problem reported by many colleagues on the list. Perhaps someone who previously complained about x2top 4.x halting should try first adding the -nopbc option to their command line and then adding the box vectors to their .gro and tell us all what happens then! :) Also, the developers might want to consider doing something about this setting and its default value. Aside from this one time, I've never had any problems with x2top 4.0.4 (especially with the -noparam option that I use all the time, just to keep things simple), and its value at generating topologies for my 2D periodic molecules cannot be overemphasized :) Hope this helps someone, Vasilii
_______________________________________________ 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/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/mailing_lists/users.php
