[gmx-users] Error in ions.tpr generation
Dear gmx experts, The ligand molecule was refined and optimized using G03 calculation and .itp was generated using the ATB server. Still, I am getting the following error, dirctly copied from the terminal. And I am unable to generate any extension files in GROMACS using this .itp. $ gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr :-) GROMACS - gmx grompp, 2018.1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par BjelkmarAldert van Buuren Rudi van Drunen Anton Feenstra Gerrit GroenhofAleksei Iupinov Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios KarkoulisPeter KassonJiri Kraus Carsten Kutzner Per Larsson Justin A. LemkulViveca Lindahl Magnus Lundborg Pieter MeulenhoffErik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter TielemanTeemu Virolainen Christian WennbergMaarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2017, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx grompp, version 2018.1 Executable: /usr/bin/gmx Data prefix: /usr Working dir: /home/ya/Desktop/Neha/fecA/gromos Command line: gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr Ignoring obsolete mdp entry 'title' NOTE 1 [file ions.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Setting the LD random seed to 49113858 Generated 165 of the 1596 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'Protein' Excluding 3 bonded neighbours molecule type '4JCP' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 2 [file topol.top, line 45350]: System has non-zero total charge: -14.00 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. Removing all charge groups because cutoff-scheme=Verlet ERROR 1 [file topol.top, line 45350]: atom O10 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 2 [file topol.top, line 45350]: atom C2 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 3 [file topol.top, line 45350]: atom O9 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 4 [file topol.top, line 45350]: atom Fe14 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 5 [file topol.top, line 45350]: atom C3 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 6 [file topol.top, line 45350]: atom C4 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 7 [file topol.top, line 45350]: atom O11 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 8 [file topol.top, line 45350]: atom H19 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 9 [file topol.top, line 45350]: atom C6 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 10 [file topol.top, line 45350]: atom O12 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 11 [file topol.top, line 45350]: atom O13 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 12 [file topol.top, line 45350]: atom C5 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 13 [file topol.top, line 45350]: atom C1 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 14 [file topol.top, line 45350]: atom O7 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 15 [file topol.top, line 45350]: atom O8 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) There were 2 notes --- Program: gmx grompp, version 2018.1 Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2137) Fatal error: There were 15 errors in input file(s) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Please help. -- 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.o
[gmx-users] Fwd: error during ions.tpr genereation.
Dear all, I want to know if there is any error in the .itp file of ligand attached here, the ligand molecule was refined and optimized using G03 calculation and .itp was generated using the ATB server. As I am unable to generate any extension files in GROMACS using this. Please help. Neha. -- 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] (no subject)
Dear Gromacs experts, I have generated topology files(.itp) of the ligand from the ATB server and everything goes well, but when it comes to generating ions.tpr file, I am getting following error. $ gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr :-) GROMACS - gmx grompp, 2018.1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par BjelkmarAldert van Buuren Rudi van Drunen Anton Feenstra Gerrit GroenhofAleksei Iupinov Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios KarkoulisPeter KassonJiri Kraus Carsten Kutzner Per Larsson Justin A. LemkulViveca Lindahl Magnus Lundborg Pieter MeulenhoffErik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter TielemanTeemu Virolainen Christian WennbergMaarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2017, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx grompp, version 2018.1 Executable: /usr/bin/gmx Data prefix: /usr Working dir: /home/ya/Desktop/Neha/fecA/gromos Command line: gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr Ignoring obsolete mdp entry 'title' NOTE 1 [file ions.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Setting the LD random seed to 49113858 Generated 165 of the 1596 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'Protein' Excluding 3 bonded neighbours molecule type '4JCP' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 2 [file topol.top, line 45350]: System has non-zero total charge: -14.00 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. Removing all charge groups because cutoff-scheme=Verlet ERROR 1 [file topol.top, line 45350]: atom O10 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 2 [file topol.top, line 45350]: atom C2 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 3 [file topol.top, line 45350]: atom O9 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 4 [file topol.top, line 45350]: atom Fe14 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 5 [file topol.top, line 45350]: atom C3 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 6 [file topol.top, line 45350]: atom C4 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 7 [file topol.top, line 45350]: atom O11 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 8 [file topol.top, line 45350]: atom H19 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 9 [file topol.top, line 45350]: atom C6 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 10 [file topol.top, line 45350]: atom O12 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 11 [file topol.top, line 45350]: atom O13 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 12 [file topol.top, line 45350]: atom C5 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 13 [file topol.top, line 45350]: atom C1 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 14 [file topol.top, line 45350]: atom O7 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) ERROR 15 [file topol.top, line 45350]: atom O8 (Res 4JCP-1) has mass 0 (state A) / 0 (state B) There were 2 notes --- Program: gmx grompp, version 2018.1 Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2137) Fatal error: There were 15 errors in input file(s) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Please help. Thanks in advance. Regards, Neha. -- 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/g
[gmx-users] Query
Dear Gromacs Experts, I want to parametrize Ferric citrate and have already performed DFT calculations using different basis sets, but I am unable to upload the refined molecule on, ATB so that I can get its topology files to proceed further. Please help. Thanks in advance. Neha. -- 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.
