Hi Marc, I think that -zeroq ignores the indexing. Using an index will extract a .tpr for the index group only, which is not what you want. There is no simple way to do what you want (using tpbconv). You'll have to modify the charge in the .top file and generate a new .tpr
Cheers, Tsjerk On Sep 30, 2011 3:05 AM, "Marc Charendoff" <mchar...@sbcglobal.net> wrote: Hello, I'm trying to turn off a Na+ charge using tpbconv in 4.5.4. There is only one Na+ counterion in my simulation. I create an index file, run tpbconv, and my output file looks like the following: [mcharend@xanadu C4_IS]$ tpbconv -s md.tpr -o mdn.tpr -n index.ndx -zeroq . . . . . . . . . . . . . . . . . . . Reading toplogy and stuff from md.tpr Reading file md.tpr, VERSION 4.5.4 (single precision) 500000 steps (1000 ps) remaining from first run. Group 0 ( System) has 3037 elements Group 1 ( Other) has 15 elements Group 2 ( DRG) has 15 elements Group 3 ( NA+) has 1 elements Group 4 ( Water) has 3021 elements Group 5 ( SOL) has 3021 elements Group 6 ( non-Water) has 16 elements Group 7 ( Ion) has 1 elements Group 8 ( DRG) has 15 elements Group 9 ( NA+) has 1 elements Group 10 ( Water_and_ions) has 3022 elements Group 11 ( NA+) has 1 elements Select a group: 9 Selected 9: 'NA+' Segmentation fault [mcharend@xanadu C4_IS]$ The bottom of my index.ndx file looks like: . . . . . . . . . . . . . . . . . [ NA+ ] 3037 Guidance appreciated. Thanks , Marc -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
-- 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/Support/Mailing_Lists/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/Support/Mailing_Lists