check your popc128.top or topol.top file ; Include POPC chain topology #include "popc.itp"
and ; Include water topology #include "gromos53a6_lipid.ff/spc.itp" and always update the no of atoms in you .gro file On Mon, Mar 16, 2015 at 10:31 AM, RINU KHATTRI <nickname.mi...@gmail.com> wrote: > firstly go back to check your system.gro file which you made bu cat > DPPC.gro new_box.gro >system.gro > remove some line between the merging of two file update the no of atoms > then do your next step > > > On Mon, Mar 16, 2015 at 9:38 AM, BAOLIN HUANG <baolin.hu...@qut.edu.au> wrote: >> Hi All, >> I am doing the GROMACS Tutorial of KALP-15 in DPPC. >> Now, I get stuck at "Note how many lipids were deleted and update the [ >> molecules ] directive of your topology accordingly. Run energy minimization. >> Then, scale down the lipids by a factor of 0.95 (assuming you have used >> default names, the result of the minimization is called "confout.gro"): perl >> inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat" >> >> The command line was gmx grompp -f minim.mdp -c system_inflated.gro -p >> topol.top -o em.tpr. And I got Fatal error: number of coordinates in >> coordinate file (system_inflated.gro, 6438) does not match topology >> (topol.top 888444) I tried to add DPPC 128 in the [ molecules ], however, I >> got Fatal error: No such moleculetype DPPC. >> >> How to update the [molecules] in topol.top? And how do I know the number of >> molecules? >> >> >> >> Kind regards, >> >> Alex Huang >> >> >> >> -- >> 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.
