In 2nd step I choose system instaed of solvent. I could not make the solute at the center.
Thanks NIlesh On Mon, October 17, 2011 11:05 am, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> Justin, >> >> >> I have 26 solute atoms and 3302 solvent atoms in my sytems (total 3328 >> atoms). >> >> >> 1. trjconv -f 3.trr -s 3.tpr -pbc mol -b 400 -e 600 -dt 1 -n 500-1.ndx >> -o >> 4-600.xtc >> here I choose group 0:system (3328 atoms) >> >> 2. trjconv -f 4-600.xtc -s 3.tpr -n 500-1.ndx -center -o 4-600-1.xtc >> >> >> For Centering I choose group: solute (26 atoms) >> For output I choose group : Solvent (3302 atoms) >> >> >> >> 3. trjconv -f 4-600-1.xtc -s 3.tpr -dump 500 -o 500-11.pdb >> >> >> Here I choose the group: 0 (system). >> >> >> I am geting for error for last command. >> >> >> Fatal error: >> Index[3302] 3303 is larger than the number of atoms in the trajectory >> file (3302). >> >> >> It look that there are no solute atoms in trajectory file. >> >> > > In step 2, you chose to save only the solvent. > > > -Justin > > > -- > ======================================== > > > 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 > > > -- 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