Re: [gmx-users] cannot load the xtc file (without PBC) to VMD
Hey again, sorry for the late reply. I meant, I didn't have the chance to do that since a .trr file after the simulation was not generated. All I had was the em.trr. Later, I solved the problem by using editconf. Thank you for your attention. On Tue, Jan 14, 2020 at 2:51 PM wrote: > I didn't get you. So your problem is solved using trr file or not? > - Message from Lalehan Ozalp - > Date: Tue, 14 Jan 2020 12:53:54 +0300 > From: Lalehan Ozalp > Reply-To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] cannot load the xtc file (without PBC) to VMD > To: gmx-us...@gromacs.org > > > 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 wrote: > > > >> Hii > >> Have you tried with the .trr file? Try the same procedure with .trr > file. > >> Thanks > >> - Message from Lalehan Ozalp - > >> Date: Mon, 13 Jan 2020 13:35:01 +0300 > >> From: Lalehan Ozalp > >> 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 - > >> -- > >> 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 > > 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 - > -- > 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.
Re: [gmx-users] cannot load the xtc file (without PBC) to VMD
I didn't get you. So your problem is solved using trr file or not? - Message from Lalehan Ozalp - Date: Tue, 14 Jan 2020 12:53:54 +0300 From: Lalehan Ozalp Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-users] cannot load the xtc file (without PBC) to VMD To: gmx-us...@gromacs.org 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 wrote: Hii Have you tried with the .trr file? Try the same procedure with .trr file. Thanks - Message from Lalehan Ozalp - Date: Mon, 13 Jan 2020 13:35:01 +0300 From: Lalehan Ozalp 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 - -- 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 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 - -- 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.
Re: [gmx-users] cannot load the xtc file (without PBC) to VMD
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 wrote: > Hii > Have you tried with the .trr file? Try the same procedure with .trr file. > Thanks > - Message from Lalehan Ozalp - > Date: Mon, 13 Jan 2020 13:35:01 +0300 > From: Lalehan Ozalp > 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 - > -- > 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.
Re: [gmx-users] cannot load the xtc file (without PBC) to VMD
Hii Have you tried with the .trr file? Try the same procedure with .trr file. Thanks - Message from Lalehan Ozalp - Date: Mon, 13 Jan 2020 13:35:01 +0300 From: Lalehan Ozalp 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 - -- 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.
Re: [gmx-users] cannot load the xtc file (without PBC) to VMD
On 1/13/20 5:35 AM, Lalehan Ozalp wrote: 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. The error implies you've loaded a mismatched coordinate file for this trajectory, or otherwise didn't save the number of coordinates you thought you did with trjconv. This is really more of a VMD problem, so you may find better support on their mailing list. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.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.
[gmx-users] cannot load the xtc file (without PBC) to VMD
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.
