[gmx-users] g_select error
hello: I am trying to use g_select to make an index file with command: g_select_mpi -f md.xtc -s npt3.pdb -on density.ndx but it failed with messages: WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Assertion failed for g in file /home/albert/Desktop/gromacs-4.6-beta3/src/gmxlib/sel dump core ? (y/n) thank you very much Albert -- 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] g_select error
On 1/10/13 4:08 AM, Albert wrote: hello: I am trying to use g_select to make an index file with command: g_select_mpi -f md.xtc -s npt3.pdb -on density.ndx but it failed with messages: WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Assertion failed for g in file /home/albert/Desktop/gromacs-4.6-beta3/src/gmxlib/sel dump core ? (y/n) Apparently whatever you're tying to select requires a .tpr file as input to work rather than a .pdb file. -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
Re: [gmx-users] g_select error
Hi, On Thu, Jan 10, 2013 at 11:08 AM, Albert mailmd2...@gmail.com wrote: I am trying to use g_select to make an index file with command: g_select_mpi -f md.xtc -s npt3.pdb -on density.ndx but it failed with messages: Assertion failed for g in file /home/albert/Desktop/gromacs-** 4.6-beta3/src/gmxlib/sel dump core ? (y/n) Could you please tell what you tried to select to cause this (the exact selection string)? Without it, it is very difficult to investigate the issue. - Teemu -- 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] g_select error
Hi, thanks for the bug report. Please let us know whether: https://gerrit.gromacs.org/#/c/2014/ fixes it. Roland On Thu, Jan 10, 2013 at 4:08 AM, Albert mailmd2...@gmail.com wrote: hello: I am trying to use g_select to make an index file with command: g_select_mpi -f md.xtc -s npt3.pdb -on density.ndx but it failed with messages: WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Assertion failed for g in file /home/albert/Desktop/gromacs-4.6-beta3/src/gmxlib/sel dump core ? (y/n) thank you very much Albert -- 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 -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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] g_select error
hello Justin: thanks for kind tips. I've tried both methods: g_select -f md.xtc -s npt3.pdb -os size.xvg -sf selection.dat g_select -f md.xtc -s npt3.pdb -os size.xvg -select 'resname SOL and name OW within 0.6 of resid 114' but they all failed with messages: log WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. selection parser: syntax error selection parser: invalid selection 'resname SOL and name OW within 0.6 of resid 114' --- Program g_select, VERSION 4.5.5 Source code file: trajana.c, line: 1310 Input error or input inconsistency: selection(s) could not be parsed For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Yeah, a Wuzz, Or a Jerk (F. Black) On 11/27/2012 01:54 AM, Justin Lemkul wrote: On 11/26/12 2:08 PM, Albert wrote: hello: I am going to calculate the number of water molecules within 6 A of residue 114 by following command: g_select -f md.xtc -s npt3.pdb -os size.xvg -select resid 114 and rdist 0.6 but it said: WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. selection parser: syntax error selection parser: invalid selection 'resid 114 and rdist 0.6' --- Program g_select, VERSION 4.5.5 Source code file: trajana.c, line: 1310 Input error or input inconsistency: selection(s) could not be parsed For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- You haven't defined rdist to actually be anything. If you need to be using multi-line selections, you should be providing a selection.dat file to -sf instead of using single-line statements to -select. Something like g_select -select 'resname SOL and name OW within 0.6 of resid 114' should do the trick, but I haven't actually tried that so I'm not 100% sure. -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
Re: [gmx-users] g_select error
On 11/27/12 9:18 AM, Albert wrote: hello Justin: thanks for kind tips. I've tried both methods: g_select -f md.xtc -s npt3.pdb -os size.xvg -sf selection.dat g_select -f md.xtc -s npt3.pdb -os size.xvg -select 'resname SOL and name OW within 0.6 of resid 114' but they all failed with messages: log WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. selection parser: syntax error selection parser: invalid selection 'resname SOL and name OW within 0.6 of resid 114' --- Program g_select, VERSION 4.5.5 Source code file: trajana.c, line: 1310 Input error or input inconsistency: selection(s) could not be parsed For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Well, like I warned, I wasn't 100% sure of the syntax, so it was no guarantee that I was right. Reading into the documentation and examples a bit, it seems that resname SOL and name OW should be enclosed within double quotes, within the single-quoted string. Otherwise, use this selection.dat file: waterO = name OW; close = waterO and within 0.6 of resid 114; close; It should be possible to do it in one line, but the above set of selections seems to work fine. -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
Re: [gmx-users] g_select error
On 11/27/2012 03:33 PM, Justin Lemkul wrote: Well, like I warned, I wasn't 100% sure of the syntax, so it was no guarantee that I was right. Reading into the documentation and examples a bit, it seems that resname SOL and name OW should be enclosed within double quotes, within the single-quoted string. Otherwise, use this selection.dat file: waterO = name OW; close = waterO and within 0.6 of resid 114; close; It should be possible to do it in one line, but the above set of selections seems to work fine. -Justin thank you so much for such kind helps. it finally works.;-) best Albert -- 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] g_select error
hello: I am going to calculate the number of water molecules within 6 A of residue 114 by following command: g_select -f md.xtc -s npt3.pdb -os size.xvg -select resid 114 and rdist 0.6 but it said: WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. selection parser: syntax error selection parser: invalid selection 'resid 114 and rdist 0.6' --- Program g_select, VERSION 4.5.5 Source code file: trajana.c, line: 1310 Input error or input inconsistency: selection(s) could not be parsed For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- It Wouldn't Hurt to Wipe Once In a While (Beavis and Butthead) -- 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] g_select error
hello: I am going to calculate the number of water molecules within 6 A of residue 114 by following command: g_select -f md.xtc -s npt3.pdb -os size.xvg -select resid 114 and rdist 0.6 but it said: WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. selection parser: syntax error selection parser: invalid selection 'resid 114 and rdist 0.6' --- Program g_select, VERSION 4.5.5 Source code file: trajana.c, line: 1310 Input error or input inconsistency: selection(s) could not be parsed For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- It Wouldn't Hurt to Wipe Once In a While (Beavis and Butthead) -- 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] g_select error
On 11/26/12 2:08 PM, Albert wrote: hello: I am going to calculate the number of water molecules within 6 A of residue 114 by following command: g_select -f md.xtc -s npt3.pdb -os size.xvg -select resid 114 and rdist 0.6 but it said: WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. selection parser: syntax error selection parser: invalid selection 'resid 114 and rdist 0.6' --- Program g_select, VERSION 4.5.5 Source code file: trajana.c, line: 1310 Input error or input inconsistency: selection(s) could not be parsed For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- You haven't defined rdist to actually be anything. If you need to be using multi-line selections, you should be providing a selection.dat file to -sf instead of using single-line statements to -select. Something like g_select -select 'resname SOL and name OW within 0.6 of resid 114' should do the trick, but I haven't actually tried that so I'm not 100% sure. -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
