Thank you, but I haven't tried with a trr file and actually the last .trr file I've produced is em.trr. Thanks,
On Mon, Jan 13, 2020 at 5:40 PM <sp...@iacs.res.in> wrote: > Hii > Have you tried with the .trr file? Try the same procedure with .trr file. > Thanks > ----- Message from Lalehan Ozalp <lalehan.oz...@gmail.com> --------- > Date: Mon, 13 Jan 2020 13:35:01 +0300 > From: Lalehan Ozalp <lalehan.oz...@gmail.com> > Reply-To: gmx-us...@gromacs.org > Subject: [gmx-users] cannot load the xtc file (without PBC) to VMD > To: gmx-us...@gromacs.org > > > 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 > > visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > send a mail to gmx-users-requ...@gromacs.org. > > ----- End message from Lalehan Ozalp <lalehan.oz...@gmail.com> ----- > -- > 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.