Re: [gmx-users] error using grompp: number of coordinates in coordinate file does not match topology
Got it already. Thank you!! > > > On 6/27/12 4:31 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: >> Hi everybody, >> I am going through the tutorial for membrane protein simulation which is >> offered by gromacs. >> I did everything just like it is described in the tutorial but when I >> want >> to do the minimization in Step 3 after packing the lipids around the >> protein I always get the error the >> "number of coordinates in coordinate file (system_inflated.gro, 9900) >> does not match topology (topol.top, 3800)" >> I understand why it is like that because I just append the membrane to >> the >> protein file but how can I also change the topology file? >> > > With a text editor. The content of the [molecules] directive must always > agree > with the contents of the coordinate file, with respect to number of > molecules > and the order in which the molecules appear. You likely need to add a > line in > this directive indicating the number of DPPC molecules, which appears to > be 122 > (9900-3800 = 6100 = 122 * 50). > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > 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 listgmx-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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
Re: [gmx-users] error using grompp: number of coordinates in coordinate file does not match topology
Hi Justin, thank you for your answer. Now it worked and I could do the minimization. But now I have the same problem again but now the difference is 630. So what I did is that I ran the minimization and everything worked. And than I used the "perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat" command of the tutorial and now I got the error: "number of coordinates in coordinate file (system_shrink1.gro, 9220) does not match topology (topol.top, 9850)" But I changed nothing at the topology file. Bests, Eva > > > On 6/27/12 4:31 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: >> Hi everybody, >> I am going through the tutorial for membrane protein simulation which is >> offered by gromacs. >> I did everything just like it is described in the tutorial but when I >> want >> to do the minimization in Step 3 after packing the lipids around the >> protein I always get the error the >> "number of coordinates in coordinate file (system_inflated.gro, 9900) >> does not match topology (topol.top, 3800)" >> I understand why it is like that because I just append the membrane to >> the >> protein file but how can I also change the topology file? >> > > With a text editor. The content of the [molecules] directive must always > agree > with the contents of the coordinate file, with respect to number of > molecules > and the order in which the molecules appear. You likely need to add a > line in > this directive indicating the number of DPPC molecules, which appears to > be 122 > (9900-3800 = 6100 = 122 * 50). > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > 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 listgmx-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 listgmx-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
Re: [gmx-users] error using grompp: number of coordinates in coordinate file does not match topology
On 6/27/12 4:31 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I am going through the tutorial for membrane protein simulation which is offered by gromacs. I did everything just like it is described in the tutorial but when I want to do the minimization in Step 3 after packing the lipids around the protein I always get the error the "number of coordinates in coordinate file (system_inflated.gro, 9900) does not match topology (topol.top, 3800)" I understand why it is like that because I just append the membrane to the protein file but how can I also change the topology file? With a text editor. The content of the [molecules] directive must always agree with the contents of the coordinate file, with respect to number of molecules and the order in which the molecules appear. You likely need to add a line in this directive indicating the number of DPPC molecules, which appears to be 122 (9900-3800 = 6100 = 122 * 50). -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 listgmx-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] error using grompp: number of coordinates in coordinate file does not match topology
Hi everybody, I am going through the tutorial for membrane protein simulation which is offered by gromacs. I did everything just like it is described in the tutorial but when I want to do the minimization in Step 3 after packing the lipids around the protein I always get the error the "number of coordinates in coordinate file (system_inflated.gro, 9900) does not match topology (topol.top, 3800)" I understand why it is like that because I just append the membrane to the protein file but how can I also change the topology file? http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html Bests, Eva -- gmx-users mailing listgmx-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
