2011/5/12 Justin A. Lemkul <jalem...@vt.edu>: > > > lina wrote: >> >> make_ndx -f your.gro/pdb -n your.ndx -o your.ndx >> >> LiGA & LİGB: > > This is not correct. You need to use | rather than &. Using logical and > (&) means the index group will contain atoms that are common to both LIGA > and LIGB. If they are distinct entities, the group will be empty. Logical > or (|) says merge the two different groups to create one unified group.
Ooops > > -Justin > >> q >> >> in grompp add -n your.ndx >> >> >> 2011/5/12 ahmet yıldırım <ahmedo...@gmail.com>: >>> >>> Dear users, >>> >>> I have two ligands. I created a special index group that merges the >>> protein, >>> LiGA and LİGB. >>> >>> I have the pr.mdp file as the following: >>> ... >>> energygrps = Protein LİGA_LİGB >>> tc-grps = Protein_LİGA_LİGB Water_and_ions >>> ... >>> >>> grompp -f pr.mdp -p topol.top -c em.gro -n index.ndx -o pr.tpr >>> Fatal error: >>> Group LİGA_LİGB not found in indexfile. >>> >>> I get the fatal error since I dont have a special index group that merges >>> LiGA and LİGB. should I create two different index file? >>> >>> Thanks in advance >>> -- >>> Ahmet YILDIRIM >>> >>> -- >>> 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 >>> >> >> >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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 > -- Best Regards, lina -- 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
