Dear all, I have a question regarding loading .xtc file (with no periodic boundary conditions) to VMD which I generated before. To this end, I had used the command: trjconv -f md_0_10.xtc -s md_30.tpr -n index.ndx -o noPBC.xtc -pbc mol -ur compact -center and selected *protein* for centering, and *system* for output. However, when I load my corresponding gro file to VMD, and then loading the xtc file above, the following error occurs:
ERROR) BaseMolecule: attempt to init atoms while structure building in progress! ERROR) Invalid number of atoms in file: 132259 Info) Using plugin xtc for coordinates from file /home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc ERROR) Incorrect number of atoms (132259) in ERROR) coordinate file /home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc ERROR) Mismatch between existing molecule or structure file atom count and coordinate or trajectory file atom count. Info) Finished with coordinate file /home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc. This is especially strange since I carried out the same procedure several times before. Additionally, I have a parallel system (with an isoenzyme of the enzyme used here, with the same cofactor and the same ligand) and the same steps worked perfectly. As a side note, this happens when I load xtc file without PBC, while does not happen when I load xtc file in the presence of PBC. Thank you so much in advance! Lalehan -- 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.
