Is there a specific reason why you're not adding the water using genbox and genion? If that's not the case you can simply delete the waters from the pdb and only convert the rest of the system. Then you can solvate, set your box boundaries and add ions.
Best, João *Joao Martins* joaomartins...@gmail.com On Tue, Aug 5, 2014 at 6:09 AM, WH <signoreguid...@163.com> wrote: > Dear Gromacs users, > > I want to use Gromacs to process a system with more than 80000 water > moelcules. However, when use pdb2gmx to deal the the pdb file, the out put > .gro file has the form like this: > 3409HOH HW234995 -5.617 -6.883 -8.771 > 3409HOH OW34996 -6.108 -6.959 -7.760 > 3409HOH HW134997 -6.107 -6.973 -7.855 > 3409HOH HW234998 -6.199 -6.971 -7.735 > 3409HOH OW34999 -4.964 -8.455 -9.110 > 3409HOH HW135000 -5.054 -8.441 -9.081 > 3409HOH HW235001 -4.939 -8.372 -9.150 > 3409HOH OW35002 -6.157 -7.576 -8.913 > 3409HOH HW135003 -6.187 -7.499 -8.962 > > Only 4 digits will be used for the residue number and 5 for the atom > number. Thus, the actual residue number and atom number cannot be written > correctly and lead to failure for the MD simulation. > Does anyone know how to fix this problem? I really appreciate it. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
