I tried restarting the whole process to go back and carefully look and make sure that nothing was spelled right. Bu I still get the same error.
On Mon, Jun 20, 2016 at 2:36 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 6/20/16 2:32 PM, Kyle Titus-Glover wrote: > >> Hey everyone, >> >> I've been working on the Justin Lemkul's 2nd tutorial and just can't seem >> to get past 2. packing the lipids around the protein and 3. solvating with >> water. The follow the instructions step by step but for some reason as I >> try to run EM with >> >> gmx grompp -f minim.mdp -c system_shrink1.gro -p topol.top -o em1.tp >> >> I get hit with this error: >> >> Fatal error: >> number of coordinates in coordinate file (system_shrink1.gro, 6400) >> does not match topology (topol.top, 6438) >> >> > 6400 is the number of atoms in the 128-lipid DPPC bilayer (128 * 50 = > 6400) so something has gone badly wrong here. Your coordinate file at this > point should have the peptide and 126 lipids; the InflateGRO output below > looks correct. Check the contents of system_shrink1.gro and make sure you > haven't perhaps accidentally renamed a file something that it shouldn't be. > > -Justin > > I figured that since my number of molecules were off that the problem was >> either the way I updated the molecules section of my topol.top fill by >> adding >> DPPC 126 >> >> after seeing this when adding lipids: >> >> There are 128 lipids... >> with 50 atoms per lipid.. >> >> Determining upper and lower leaflet... >> 64 lipids in the upper... >> 64 lipids in the lower leaflet >> >> Centering protein.... >> Checking for overlap.... >> ...this might actually take a while.... >> 100 % done... >> There are 2 lipids within cut-off range... >> 1 will be removed from the upper leaflet... >> 1 will be removed from the lower leaflet... >> >> But for some reason I can't seem to start the EM iterations because of >> this >> error. >> >> Sincerely, >> >> Kyle Titus-Glover >> Virginia Tech '17 | Engineering Science & Mechanics >> Dean's Research Assistant, College of Engineering >> 443-802-4058 >> >> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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.