[gmx-users] Grompp note
Hello, I am running a equilibration simulation for ionic liquids at 400 K. I am getting following note. The sum of the two largest charge group radii (0.213127) is larger than rlist (1.00) - rvdw (0.90) Could you tell what is the problem? I am using Gromacs VERSION 4.5.5 . I used the following mdp file. ; RUN CONTROL PARAMETERS = integrator = sd ; start time and timestep in ps = tinit= 0 dt = 0.001 nsteps = 20 ; number of steps for center of mass motion removal = nstcomm = 100 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 0 nstvout = 0 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 5000 nstenergy= 1000 ; Output frequency and precision for xtc file = nstxtcout= 5000 xtc-precision= 1000 ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ;OPTIONS FOR TEMPERATURE COUPLING tc_grps = system tau_t= 0.1 ref_t= 400 ;OPTIONS FOR PRESSURE COUPLING Pcoupl = berendsen tau_p= 0.5 compressibility = 4.5e-05 ref_p= 1.0 ; OPTIONS FOR BONDS = constraints = hbonds ; Type of constraint algorithm = constraint-algorithm = Lincs ; Do not constrain the start configuration = unconstrained-start = no ; Relative tolerance of shake = shake-tol= 0.0001 ; Highest order in the expansion of the constraint coupling matrix = lincs-order = 12 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs-warnangle = 30 ; Periodic boundary conditions: xyz or none = pbc = xyz ; nblist cut-off = rlist= 1.0 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = pme ;rcoulomb-switch = 0 rcoulomb = 1.0 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon-r= 1 ; Method for doing Van der Waals = vdw-type = switch ; cut-off lengths= rvdw-switch = 0.8 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = EnerPres ; Spacing for the PME/PPPM FFT grid = fourierspacing = 0.1 ; FFT grid size, when a value is 0 fourierspacing will be used = fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters = pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no ; Free energy control stuff free_energy = no Nilesh -- 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] Grompp note
On 10/31/13 10:30 AM, Nilesh Dhumal wrote: Hello, I am running a equilibration simulation for ionic liquids at 400 K. I am getting following note. The sum of the two largest charge group radii (0.213127) is larger than rlist (1.00) - rvdw (0.90) Could you tell what is the problem? I am using Gromacs VERSION 4.5.5 . http://www.gromacs.org/Documentation/Errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb Also see the numerous discussions on this topic in the list archive. -Justin I used the following mdp file. ; RUN CONTROL PARAMETERS = integrator = sd ; start time and timestep in ps = tinit= 0 dt = 0.001 nsteps = 20 ; number of steps for center of mass motion removal = nstcomm = 100 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 0 nstvout = 0 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 5000 nstenergy= 1000 ; Output frequency and precision for xtc file = nstxtcout= 5000 xtc-precision= 1000 ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ;OPTIONS FOR TEMPERATURE COUPLING tc_grps = system tau_t= 0.1 ref_t= 400 ;OPTIONS FOR PRESSURE COUPLING Pcoupl = berendsen tau_p= 0.5 compressibility = 4.5e-05 ref_p= 1.0 ; OPTIONS FOR BONDS = constraints = hbonds ; Type of constraint algorithm = constraint-algorithm = Lincs ; Do not constrain the start configuration = unconstrained-start = no ; Relative tolerance of shake = shake-tol= 0.0001 ; Highest order in the expansion of the constraint coupling matrix = lincs-order = 12 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs-warnangle = 30 ; Periodic boundary conditions: xyz or none = pbc = xyz ; nblist cut-off = rlist= 1.0 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = pme ;rcoulomb-switch = 0 rcoulomb = 1.0 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon-r= 1 ; Method for doing Van der Waals = vdw-type = switch ; cut-off lengths= rvdw-switch = 0.8 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = EnerPres ; Spacing for the PME/PPPM FFT grid = fourierspacing = 0.1 ; FFT grid size, when a value is 0 fourierspacing will be used = fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters = pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no ; Free energy control stuff free_energy = no Nilesh -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Grompp note
Could you tell how can I get rid of following warning? WARNING 1 [file test.top, line 263]: The bond in molecule-type BMI between atoms 10 C10 and 23 H23 has an estimated oscillational period of 1.2e-03 ps, which is less than 5 times the time step of 1.0e-03 ps. Maybe you forgot to change the constraints mdp option. On 10/31/13 10:30 AM, Nilesh Dhumal wrote: Hello, I am running a equilibration simulation for ionic liquids at 400 K. I am getting following note. The sum of the two largest charge group radii (0.213127) is larger than rlist (1.00) - rvdw (0.90) Could you tell what is the problem? I am using Gromacs VERSION 4.5.5 . http://www.gromacs.org/Documentation/Errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb Also see the numerous discussions on this topic in the list archive. -Justin I used the following mdp file. ; RUN CONTROL PARAMETERS = integrator = sd ; start time and timestep in ps = tinit= 0 dt = 0.001 nsteps = 20 ; number of steps for center of mass motion removal = nstcomm = 100 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 0 nstvout = 0 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 5000 nstenergy= 1000 ; Output frequency and precision for xtc file = nstxtcout= 5000 xtc-precision= 1000 ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ;OPTIONS FOR TEMPERATURE COUPLING tc_grps = system tau_t= 0.1 ref_t= 400 ;OPTIONS FOR PRESSURE COUPLING Pcoupl = berendsen tau_p= 0.5 compressibility = 4.5e-05 ref_p= 1.0 ; OPTIONS FOR BONDS = constraints = hbonds ; Type of constraint algorithm = constraint-algorithm = Lincs ; Do not constrain the start configuration = unconstrained-start = no ; Relative tolerance of shake = shake-tol= 0.0001 ; Highest order in the expansion of the constraint coupling matrix = lincs-order = 12 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs-warnangle = 30 ; Periodic boundary conditions: xyz or none = pbc = xyz ; nblist cut-off = rlist= 1.0 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = pme ;rcoulomb-switch = 0 rcoulomb = 1.0 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon-r= 1 ; Method for doing Van der Waals = vdw-type = switch ; cut-off lengths= rvdw-switch = 0.8 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = EnerPres ; Spacing for the PME/PPPM FFT grid = fourierspacing = 0.1 ; FFT grid size, when a value is 0 fourierspacing will be used = fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters = pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no ; Free energy control stuff free_energy = no Nilesh -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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 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] Grompp note
On 10/31/13 11:40 AM, Nilesh Dhumal wrote: Could you tell how can I get rid of following warning? WARNING 1 [file test.top, line 263]: The bond in molecule-type BMI between atoms 10 C10 and 23 H23 has an estimated oscillational period of 1.2e-03 ps, which is less than 5 times the time step of 1.0e-03 ps. Maybe you forgot to change the constraints mdp option. The relationship between high-frequency vibrations and the chosen timestep is a fundamental point in MD simulations. Any textbook covers it. There are even a few hints in the Gromacs manual. -Justin On 10/31/13 10:30 AM, Nilesh Dhumal wrote: Hello, I am running a equilibration simulation for ionic liquids at 400 K. I am getting following note. The sum of the two largest charge group radii (0.213127) is larger than rlist (1.00) - rvdw (0.90) Could you tell what is the problem? I am using Gromacs VERSION 4.5.5 . http://www.gromacs.org/Documentation/Errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb Also see the numerous discussions on this topic in the list archive. -Justin I used the following mdp file. ; RUN CONTROL PARAMETERS = integrator = sd ; start time and timestep in ps = tinit= 0 dt = 0.001 nsteps = 20 ; number of steps for center of mass motion removal = nstcomm = 100 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 0 nstvout = 0 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 5000 nstenergy= 1000 ; Output frequency and precision for xtc file = nstxtcout= 5000 xtc-precision= 1000 ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ;OPTIONS FOR TEMPERATURE COUPLING tc_grps = system tau_t= 0.1 ref_t= 400 ;OPTIONS FOR PRESSURE COUPLING Pcoupl = berendsen tau_p= 0.5 compressibility = 4.5e-05 ref_p= 1.0 ; OPTIONS FOR BONDS = constraints = hbonds ; Type of constraint algorithm = constraint-algorithm = Lincs ; Do not constrain the start configuration = unconstrained-start = no ; Relative tolerance of shake = shake-tol= 0.0001 ; Highest order in the expansion of the constraint coupling matrix = lincs-order = 12 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs-warnangle = 30 ; Periodic boundary conditions: xyz or none = pbc = xyz ; nblist cut-off = rlist= 1.0 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = pme ;rcoulomb-switch = 0 rcoulomb = 1.0 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon-r= 1 ; Method for doing Van der Waals = vdw-type = switch ; cut-off lengths= rvdw-switch = 0.8 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = EnerPres ; Spacing for the PME/PPPM FFT grid = fourierspacing = 0.1 ; FFT grid size, when a value is 0 fourierspacing will be used = fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters = pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no ; Free energy control stuff free_energy = no Nilesh -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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 -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201
[gmx-users] grompp Warning: atom name 20 in p2.top and p2.pdb does not match
Hello, I am doing energy minimization for my system. I am getting following warnings Warning: atom name 20 in p2.top and p2.pdb does not match (C - S20) Warning: atom name 21 in p2.top and p2.pdb does not match (C2 - O21) Warning: atom name 22 in p2.top and p2.pdb does not match (N3 - O22) Warning: atom name 23 in p2.top and p2.pdb does not match (C4 - O23) Warning: atom name 24 in p2.top and p2.pdb does not match (N5 - O24) Warning: atom name 25 in p2.top and p2.pdb does not match (C6 - C25) Warning: atom name 26 in p2.top and p2.pdb does not match (C7 - C26) Warning: atom name 27 in p2.top and p2.pdb does not match (C8 - H27) Warning: atom name 28 in p2.top and p2.pdb does not match (H9 - H28) Warning: atom name 29 in p2.top and p2.pdb does not match (H10 - H29) Warning: atom name 30 in p2.top and p2.pdb does not match (H11 - H30) Warning: atom name 31 in p2.top and p2.pdb does not match (H12 - H31) Warning: atom name 32 in p2.top and p2.pdb does not match (H13 - C) Warning: atom name 33 in p2.top and p2.pdb does not match (H14 - C2) Warning: atom name 34 in p2.top and p2.pdb does not match (H15 - N3) Warning: atom name 35 in p2.top and p2.pdb does not match (H16 - C4) Warning: atom name 36 in p2.top and p2.pdb does not match (H17 - N5) Warning: atom name 37 in p2.top and p2.pdb does not match (H18 - C6) Warning: atom name 38 in p2.top and p2.pdb does not match (H19 - C7) Warning: atom name 39 in p2.top and p2.pdb does not match (S20 - C8) Here is .pdb file TITLE Protein REMARKTHIS IS A SIMULATION BOX CRYST1 34.775 34.775 34.775 90.00 90.00 90.00 P 1 1 MODEL1 ATOM 1 C EMI 1 4.659 30.489 15.747 1.00 0.00 ATOM 2 C2 EMI 1 5.238 30.284 14.495 1.00 0.00 ATOM 3 N3 EMI 1 6.415 30.946 14.495 1.00 0.00 ATOM 4 C4 EMI 1 6.627 31.499 15.682 1.00 0.00 ATOM 5 N5 EMI 1 5.595 31.153 16.470 1.00 0.00 ATOM 6 C6 EMI 1 5.462 31.463 17.884 1.00 0.00 ATOM 7 C7 EMI 1 4.501 30.509 18.615 1.00 0.00 ATOM 8 C8 EMI 1 7.321 30.993 13.363 1.00 0.00 ATOM 9 H9 EMI 1 3.672 30.193 16.130 1.00 0.00 ATOM 10 H10 EMI 1 4.839 29.853 13.640 1.00 0.00 ATOM 11 H11 EMI 1 7.514 32.004 16.038 1.00 0.00 ATOM 12 H12 EMI 1 7.951 31.796 13.329 1.00 0.00 ATOM 13 H13 EMI 1 7.967 30.145 13.270 1.00 0.00 ATOM 14 H14 EMI 1 6.890 31.170 12.362 1.00 0.00 ATOM 15 H15 EMI 1 5.214 32.491 18.125 1.00 0.00 ATOM 16 H16 EMI 1 6.495 31.335 18.302 1.00 0.00 ATOM 17 H17 EMI 1 4.834 29.492 18.590 1.00 0.00 ATOM 18 H18 EMI 1 4.337 30.767 19.685 1.00 0.00 ATOM 19 H19 EMI 1 3.486 30.669 18.338 1.00 0.00 ATOM 20 S20 ETS 2 13.817 2.976 33.669 1.00 0.00 ATOM 21 O21 ETS 2 15.031 2.685 34.347 1.00 0.00 ATOM 22 O22 ETS 2 14.005 3.313 32.237 1.00 0.00 ATOM 23 O23 ETS 2 12.775 1.970 33.860 1.00 0.00 ATOM 24 O24 ETS 2 13.303 4.314 34.278 1.00 0.00 ATOM 25 C25 ETS 2 12.361 5.280 33.781 1.00 0.00 ATOM 26 C26 ETS 2 12.277 6.501 34.666 1.00 0.00 ATOM 27 H27 ETS 2 12.582 5.675 32.806 1.00 0.00 ATOM 28 H28 ETS 2 11.377 4.787 33.550 1.00 0.00 ATOM 29 H29 ETS 2 11.686 6.245 35.492 1.00 0.00 ATOM 30 H30 ETS 2 13.256 6.810 34.975 1.00 0.00 ATOM 31 H31 ETS 2 11.856 7.349 34.171 1.00 0.00 ATOM 32 C EMI 3 25.075 29.706 5.816 1.00 0.00 ATOM 33 C2 EMI 3 24.256 29.876 6.894 1.00 0.00 and .top file is [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_561 1EMI C 1 -0.13 12.011 ; qtot -0.13 2 opls_561 1EMI C2 2 -0.13 12.011 ; qtot -0.26 3 opls_557 1EMI N3 3 0.1514.0067 ; qtot -0.11 4 opls_558 1EMI C4 4 -0.11 12.011 ; qtot -0.22 5 opls_557 1EMI N5 5 0.1514.0067 ; qtot -0.07 6 opls_136 1EMI C6 6 -0.05 12.011 ; qtot -0.12 7 opls_135 1EMI C7 7 -0.17 12.011 ; qtot -0.29 8 opls_135 1EMI C8 8 -0.17 12.011 ; qtot -0.46 9 opls_564 1EMI H9 9 0.21 1.008 ; qtot -0.25 10 opls_564 1EMIH10 9 0.21 1.008 ; qtot -0.04 11 opls_563 1EMIH11 9 0.21 1.008 ; qtot 0.17 12 opls_140 1EMIH12 10 0.13 1.008 ; qtot 0.3 13 opls_140 1EMIH13
Re: [gmx-users] grompp Warning: atom name 20 in p2.top and p2.pdb does not match
On 9/22/13 7:13 PM, Nilesh Dhumal wrote: Hello, I am doing energy minimization for my system. I am getting following warnings Warning: atom name 20 in p2.top and p2.pdb does not match (C - S20) Warning: atom name 21 in p2.top and p2.pdb does not match (C2 - O21) Warning: atom name 22 in p2.top and p2.pdb does not match (N3 - O22) Warning: atom name 23 in p2.top and p2.pdb does not match (C4 - O23) Warning: atom name 24 in p2.top and p2.pdb does not match (N5 - O24) Warning: atom name 25 in p2.top and p2.pdb does not match (C6 - C25) Warning: atom name 26 in p2.top and p2.pdb does not match (C7 - C26) Warning: atom name 27 in p2.top and p2.pdb does not match (C8 - H27) Warning: atom name 28 in p2.top and p2.pdb does not match (H9 - H28) Warning: atom name 29 in p2.top and p2.pdb does not match (H10 - H29) Warning: atom name 30 in p2.top and p2.pdb does not match (H11 - H30) Warning: atom name 31 in p2.top and p2.pdb does not match (H12 - H31) Warning: atom name 32 in p2.top and p2.pdb does not match (H13 - C) Warning: atom name 33 in p2.top and p2.pdb does not match (H14 - C2) Warning: atom name 34 in p2.top and p2.pdb does not match (H15 - N3) Warning: atom name 35 in p2.top and p2.pdb does not match (H16 - C4) Warning: atom name 36 in p2.top and p2.pdb does not match (H17 - N5) Warning: atom name 37 in p2.top and p2.pdb does not match (H18 - C6) Warning: atom name 38 in p2.top and p2.pdb does not match (H19 - C7) Warning: atom name 39 in p2.top and p2.pdb does not match (S20 - C8) Here is .pdb file TITLE Protein REMARKTHIS IS A SIMULATION BOX CRYST1 34.775 34.775 34.775 90.00 90.00 90.00 P 1 1 MODEL1 ATOM 1 C EMI 1 4.659 30.489 15.747 1.00 0.00 ATOM 2 C2 EMI 1 5.238 30.284 14.495 1.00 0.00 ATOM 3 N3 EMI 1 6.415 30.946 14.495 1.00 0.00 ATOM 4 C4 EMI 1 6.627 31.499 15.682 1.00 0.00 ATOM 5 N5 EMI 1 5.595 31.153 16.470 1.00 0.00 ATOM 6 C6 EMI 1 5.462 31.463 17.884 1.00 0.00 ATOM 7 C7 EMI 1 4.501 30.509 18.615 1.00 0.00 ATOM 8 C8 EMI 1 7.321 30.993 13.363 1.00 0.00 ATOM 9 H9 EMI 1 3.672 30.193 16.130 1.00 0.00 ATOM 10 H10 EMI 1 4.839 29.853 13.640 1.00 0.00 ATOM 11 H11 EMI 1 7.514 32.004 16.038 1.00 0.00 ATOM 12 H12 EMI 1 7.951 31.796 13.329 1.00 0.00 ATOM 13 H13 EMI 1 7.967 30.145 13.270 1.00 0.00 ATOM 14 H14 EMI 1 6.890 31.170 12.362 1.00 0.00 ATOM 15 H15 EMI 1 5.214 32.491 18.125 1.00 0.00 ATOM 16 H16 EMI 1 6.495 31.335 18.302 1.00 0.00 ATOM 17 H17 EMI 1 4.834 29.492 18.590 1.00 0.00 ATOM 18 H18 EMI 1 4.337 30.767 19.685 1.00 0.00 ATOM 19 H19 EMI 1 3.486 30.669 18.338 1.00 0.00 ATOM 20 S20 ETS 2 13.817 2.976 33.669 1.00 0.00 ATOM 21 O21 ETS 2 15.031 2.685 34.347 1.00 0.00 ATOM 22 O22 ETS 2 14.005 3.313 32.237 1.00 0.00 ATOM 23 O23 ETS 2 12.775 1.970 33.860 1.00 0.00 ATOM 24 O24 ETS 2 13.303 4.314 34.278 1.00 0.00 ATOM 25 C25 ETS 2 12.361 5.280 33.781 1.00 0.00 ATOM 26 C26 ETS 2 12.277 6.501 34.666 1.00 0.00 ATOM 27 H27 ETS 2 12.582 5.675 32.806 1.00 0.00 ATOM 28 H28 ETS 2 11.377 4.787 33.550 1.00 0.00 ATOM 29 H29 ETS 2 11.686 6.245 35.492 1.00 0.00 ATOM 30 H30 ETS 2 13.256 6.810 34.975 1.00 0.00 ATOM 31 H31 ETS 2 11.856 7.349 34.171 1.00 0.00 ATOM 32 C EMI 3 25.075 29.706 5.816 1.00 0.00 ATOM 33 C2 EMI 3 24.256 29.876 6.894 1.00 0.00 and .top file is [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_561 1EMI C 1 -0.13 12.011 ; qtot -0.13 2 opls_561 1EMI C2 2 -0.13 12.011 ; qtot -0.26 3 opls_557 1EMI N3 3 0.1514.0067 ; qtot -0.11 4 opls_558 1EMI C4 4 -0.11 12.011 ; qtot -0.22 5 opls_557 1EMI N5 5 0.1514.0067 ; qtot -0.07 6 opls_136 1EMI C6 6 -0.05 12.011 ; qtot -0.12 7 opls_135 1EMI C7 7 -0.17 12.011 ; qtot -0.29 8 opls_135 1EMI C8 8 -0.17 12.011 ; qtot -0.46 9 opls_564 1EMI H9 9 0.21 1.008 ; qtot -0.25 10 opls_564 1EMIH10 9 0.21 1.008 ; qtot -0.04 11 opls_563 1EMIH11 9 0.21 1.008 ; qtot 0.17 12 opls_140 1EMIH12 10 0.13
Re: [gmx-users] grompp Warning: atom name 20 in p2.top and p2.pdb does not match
On 9/22/13 8:54 PM, Nilesh Dhumal wrote: Sorry to send email directly to your email address. Because of attachments it not going through gmx_users. The proper protocol is to post the files via publicly accessible URL so that anyone interested in helping may assist. attached the topology file p2.top, force field file glu-emi_lopes.itp and etso4.itp molecule files emi.itp and ets.itp file. I updated ffoplsaa.itp file as #include glu-emi_lop.itp #include etso4.itp #include emi.itp ;#include glu-emi_lop-modify.itp ;#include dmso-nilesh.itp ;#include ffoplsaanb.itp ;#include ffoplsaabon.itp ;#include pf6_opls.itp ;#include solvent.itp ;#include bmi1.itp ;#include acetate.itp ;#include pf6.itp #include ets.itp ;#include water-flexiable.itp I'm not willing to hack my own force field files to make this work. If you can provide a clean version, i.e. via a complete directory of modified files and/or post-processed topology from grompp -pp, that would be more useful and less error-prone. Note that you did not send the coordinate file, which is critical information. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] grompp Warning: atom name 20 in p2.top and p2.pdb does not match
Sorry to paste big files here. (.pdb file and processed.top ) pdb file. TITLE Protein REMARKTHIS IS A SIMULATION BOX CRYST1 34.775 34.775 34.775 90.00 90.00 90.00 P 1 1 MODEL1 ATOM 1 C EMI 1 4.659 30.489 15.747 1.00 0.00 ATOM 2 C2 EMI 1 5.238 30.284 14.495 1.00 0.00 ATOM 3 N3 EMI 1 6.415 30.946 14.495 1.00 0.00 ATOM 4 C4 EMI 1 6.627 31.499 15.682 1.00 0.00 ATOM 5 N5 EMI 1 5.595 31.153 16.470 1.00 0.00 ATOM 6 C6 EMI 1 5.462 31.463 17.884 1.00 0.00 ATOM 7 C7 EMI 1 4.501 30.509 18.615 1.00 0.00 ATOM 8 C8 EMI 1 7.321 30.993 13.363 1.00 0.00 ATOM 9 H9 EMI 1 3.672 30.193 16.130 1.00 0.00 ATOM 10 H10 EMI 1 4.839 29.853 13.640 1.00 0.00 ATOM 11 H11 EMI 1 7.514 32.004 16.038 1.00 0.00 ATOM 12 H12 EMI 1 7.951 31.796 13.329 1.00 0.00 ATOM 13 H13 EMI 1 7.967 30.145 13.270 1.00 0.00 ATOM 14 H14 EMI 1 6.890 31.170 12.362 1.00 0.00 ATOM 15 H15 EMI 1 5.214 32.491 18.125 1.00 0.00 ATOM 16 H16 EMI 1 6.495 31.335 18.302 1.00 0.00 ATOM 17 H17 EMI 1 4.834 29.492 18.590 1.00 0.00 ATOM 18 H18 EMI 1 4.337 30.767 19.685 1.00 0.00 ATOM 19 H19 EMI 1 3.486 30.669 18.338 1.00 0.00 ATOM 20 S20 ETS 2 13.817 2.976 33.669 1.00 0.00 ATOM 21 O21 ETS 2 15.031 2.685 34.347 1.00 0.00 ATOM 22 O22 ETS 2 14.005 3.313 32.237 1.00 0.00 ATOM 23 O23 ETS 2 12.775 1.970 33.860 1.00 0.00 ATOM 24 O24 ETS 2 13.303 4.314 34.278 1.00 0.00 ATOM 25 C25 ETS 2 12.361 5.280 33.781 1.00 0.00 ATOM 26 C26 ETS 2 12.277 6.501 34.666 1.00 0.00 ATOM 27 H27 ETS 2 12.582 5.675 32.806 1.00 0.00 ATOM 28 H28 ETS 2 11.377 4.787 33.550 1.00 0.00 ATOM 29 H29 ETS 2 11.686 6.245 35.492 1.00 0.00 ATOM 30 H30 ETS 2 13.256 6.810 34.975 1.00 0.00 ATOM 31 H31 ETS 2 11.856 7.349 34.171 1.00 0.00 ATOM 32 C EMI 3 25.075 29.706 5.816 1.00 0.00 ATOM 33 C2 EMI 3 24.256 29.876 6.894 1.00 0.00 ATOM 34 N3 EMI 3 25.074 30.288 7.940 1.00 0.00 ATOM 35 C4 EMI 3 26.335 30.336 7.464 1.00 0.00 ATOM 36 N5 EMI 3 26.369 29.867 6.216 1.00 0.00 ATOM 37 C6 EMI 3 27.586 29.761 5.460 1.00 0.00 ATOM 38 C7 EMI 3 27.397 29.088 4.106 1.00 0.00 ATOM 39 C8 EMI 3 24.601 30.404 9.351 1.00 0.00 ATOM 40 H9 EMI 3 24.815 29.446 4.790 1.00 0.00 ATOM 41 H10 EMI 3 23.203 29.817 6.920 1.00 0.00 ATOM 42 H11 EMI 3 27.238 30.558 8.074 1.00 0.00 ATOM 43 H12 EMI 3 24.321 29.435 9.759 1.00 0.00 ATOM 44 H13 EMI 3 25.411 30.876 9.880 1.00 0.00 ATOM 45 H14 EMI 3 23.735 31.092 9.515 1.00 0.00 ATOM 46 H15 EMI 3 28.216 29.130 6.169 1.00 0.00 ATOM 47 H16 EMI 3 28.027 30.763 5.434 1.00 0.00 ATOM 48 H17 EMI 3 26.886 29.695 3.344 1.00 0.00 ATOM 49 H18 EMI 3 28.366 28.886 3.715 1.00 0.00 ATOM 50 H19 EMI 3 26.842 28.200 3.880 1.00 0.00 ATOM 51 S20 ETS 4 26.876 17.203 7.791 1.00 0.00 ATOM 52 O21 ETS 4 28.030 16.750 7.061 1.00 0.00 ATOM 53 O22 ETS 4 25.656 16.428 7.528 1.00 0.00 ATOM 54 O23 ETS 4 27.112 17.470 9.202 1.00 0.00 ATOM 55 O24 ETS 4 26.578 18.733 7.129 1.00 0.00 ATOM 56 C25 ETS 4 26.215 18.995 5.843 1.00 0.00 ATOM 57 C26 ETS 4 27.436 19.133 4.921 1.00 0.00 ATOM 58 H27 ETS 4 25.607 18.170 5.486 1.00 0.00 ATOM 59 H28 ETS 4 25.530 19.872 5.774 1.00 0.00 ATOM 60 H29 ETS 4 28.107 19.910 5.179 1.00 0.00 ATOM 61 H30 ETS 4 27.944 18.247 4.832 1.00 0.00 ATOM 62 H31 ETS 4 27.138 19.330 3.927 1.00 0.00 TER ENDMDL processed.top ; ; File 'p2.top' was generated ; By user: ndhumal (36026) ; On host: c63 ; At date: Sun Sep 22 21:03:07 2013 ; ; This is your topology file ; Protein ; ; Include forcefield parameters ; This force field uses a format that requires Gromacs 3.1.4 or later. ; ; References for the OPLS-AA force field: ; ; W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives, ; J. Am. Chem. Soc. 118, 11225-11236 (1996). ; W. L. Jorgensen and N. A. McDonald, Theochem 424, 145-155 (1998). ; W. L. Jorgensen and N. A. McDonald, J. Phys. Chem. B 102, 8049-8059 (1998). ; R. C. Rizzo and
Re: [gmx-users] grompp Warning: atom name 20 in p2.top and p2.pdb does not match
On 9/22/13 9:18 PM, Nilesh Dhumal wrote: Sorry to paste big files here. (.pdb file and processed.top ) pdb file. TITLE Protein REMARKTHIS IS A SIMULATION BOX CRYST1 34.775 34.775 34.775 90.00 90.00 90.00 P 1 1 MODEL1 ATOM 1 C EMI 1 4.659 30.489 15.747 1.00 0.00 ATOM 2 C2 EMI 1 5.238 30.284 14.495 1.00 0.00 ATOM 3 N3 EMI 1 6.415 30.946 14.495 1.00 0.00 ATOM 4 C4 EMI 1 6.627 31.499 15.682 1.00 0.00 ATOM 5 N5 EMI 1 5.595 31.153 16.470 1.00 0.00 ATOM 6 C6 EMI 1 5.462 31.463 17.884 1.00 0.00 ATOM 7 C7 EMI 1 4.501 30.509 18.615 1.00 0.00 ATOM 8 C8 EMI 1 7.321 30.993 13.363 1.00 0.00 ATOM 9 H9 EMI 1 3.672 30.193 16.130 1.00 0.00 ATOM 10 H10 EMI 1 4.839 29.853 13.640 1.00 0.00 ATOM 11 H11 EMI 1 7.514 32.004 16.038 1.00 0.00 ATOM 12 H12 EMI 1 7.951 31.796 13.329 1.00 0.00 ATOM 13 H13 EMI 1 7.967 30.145 13.270 1.00 0.00 ATOM 14 H14 EMI 1 6.890 31.170 12.362 1.00 0.00 ATOM 15 H15 EMI 1 5.214 32.491 18.125 1.00 0.00 ATOM 16 H16 EMI 1 6.495 31.335 18.302 1.00 0.00 ATOM 17 H17 EMI 1 4.834 29.492 18.590 1.00 0.00 ATOM 18 H18 EMI 1 4.337 30.767 19.685 1.00 0.00 ATOM 19 H19 EMI 1 3.486 30.669 18.338 1.00 0.00 ATOM 20 S20 ETS 2 13.817 2.976 33.669 1.00 0.00 ATOM 21 O21 ETS 2 15.031 2.685 34.347 1.00 0.00 ATOM 22 O22 ETS 2 14.005 3.313 32.237 1.00 0.00 ATOM 23 O23 ETS 2 12.775 1.970 33.860 1.00 0.00 ATOM 24 O24 ETS 2 13.303 4.314 34.278 1.00 0.00 ATOM 25 C25 ETS 2 12.361 5.280 33.781 1.00 0.00 ATOM 26 C26 ETS 2 12.277 6.501 34.666 1.00 0.00 ATOM 27 H27 ETS 2 12.582 5.675 32.806 1.00 0.00 ATOM 28 H28 ETS 2 11.377 4.787 33.550 1.00 0.00 ATOM 29 H29 ETS 2 11.686 6.245 35.492 1.00 0.00 ATOM 30 H30 ETS 2 13.256 6.810 34.975 1.00 0.00 ATOM 31 H31 ETS 2 11.856 7.349 34.171 1.00 0.00 ATOM 32 C EMI 3 25.075 29.706 5.816 1.00 0.00 ATOM 33 C2 EMI 3 24.256 29.876 6.894 1.00 0.00 ATOM 34 N3 EMI 3 25.074 30.288 7.940 1.00 0.00 ATOM 35 C4 EMI 3 26.335 30.336 7.464 1.00 0.00 ATOM 36 N5 EMI 3 26.369 29.867 6.216 1.00 0.00 ATOM 37 C6 EMI 3 27.586 29.761 5.460 1.00 0.00 ATOM 38 C7 EMI 3 27.397 29.088 4.106 1.00 0.00 ATOM 39 C8 EMI 3 24.601 30.404 9.351 1.00 0.00 ATOM 40 H9 EMI 3 24.815 29.446 4.790 1.00 0.00 ATOM 41 H10 EMI 3 23.203 29.817 6.920 1.00 0.00 ATOM 42 H11 EMI 3 27.238 30.558 8.074 1.00 0.00 ATOM 43 H12 EMI 3 24.321 29.435 9.759 1.00 0.00 ATOM 44 H13 EMI 3 25.411 30.876 9.880 1.00 0.00 ATOM 45 H14 EMI 3 23.735 31.092 9.515 1.00 0.00 ATOM 46 H15 EMI 3 28.216 29.130 6.169 1.00 0.00 ATOM 47 H16 EMI 3 28.027 30.763 5.434 1.00 0.00 ATOM 48 H17 EMI 3 26.886 29.695 3.344 1.00 0.00 ATOM 49 H18 EMI 3 28.366 28.886 3.715 1.00 0.00 ATOM 50 H19 EMI 3 26.842 28.200 3.880 1.00 0.00 ATOM 51 S20 ETS 4 26.876 17.203 7.791 1.00 0.00 ATOM 52 O21 ETS 4 28.030 16.750 7.061 1.00 0.00 ATOM 53 O22 ETS 4 25.656 16.428 7.528 1.00 0.00 ATOM 54 O23 ETS 4 27.112 17.470 9.202 1.00 0.00 ATOM 55 O24 ETS 4 26.578 18.733 7.129 1.00 0.00 ATOM 56 C25 ETS 4 26.215 18.995 5.843 1.00 0.00 ATOM 57 C26 ETS 4 27.436 19.133 4.921 1.00 0.00 ATOM 58 H27 ETS 4 25.607 18.170 5.486 1.00 0.00 ATOM 59 H28 ETS 4 25.530 19.872 5.774 1.00 0.00 ATOM 60 H29 ETS 4 28.107 19.910 5.179 1.00 0.00 ATOM 61 H30 ETS 4 27.944 18.247 4.832 1.00 0.00 ATOM 62 H31 ETS 4 27.138 19.330 3.927 1.00 0.00 TER ENDMDL snip [ molecules ] ; Compound#mols EMI 2 ETS 2 As I suspected, your molecules are simply out of order. Your topology specifies EMI-EMI-ETS-ETS, but the coordinate file lists the molecules as EMI-ETS-EMI-ETS, hence the mismatch. The Protein [moleculetype] seems superfluous, but would be the appropriate solution for this case since it specifies EMI-ETS-EMI-ETS all in one [moleculetype] definition. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department
Re: [gmx-users] grompp Warning: atom name 20 in p2.top and p2.pdb does not match
Thanks. I have total 128 EMI and 128 ETS. To find the solution I test for 2 EMI and 2 ETS. How can I define for 128 EMI and 128 ETS ? Nilesh On 9/22/13 9:18 PM, Nilesh Dhumal wrote: Sorry to paste big files here. (.pdb file and processed.top ) pdb file. TITLE Protein REMARKTHIS IS A SIMULATION BOX CRYST1 34.775 34.775 34.775 90.00 90.00 90.00 P 1 1 MODEL1 ATOM 1 C EMI 1 4.659 30.489 15.747 1.00 0.00 ATOM 2 C2 EMI 1 5.238 30.284 14.495 1.00 0.00 ATOM 3 N3 EMI 1 6.415 30.946 14.495 1.00 0.00 ATOM 4 C4 EMI 1 6.627 31.499 15.682 1.00 0.00 ATOM 5 N5 EMI 1 5.595 31.153 16.470 1.00 0.00 ATOM 6 C6 EMI 1 5.462 31.463 17.884 1.00 0.00 ATOM 7 C7 EMI 1 4.501 30.509 18.615 1.00 0.00 ATOM 8 C8 EMI 1 7.321 30.993 13.363 1.00 0.00 ATOM 9 H9 EMI 1 3.672 30.193 16.130 1.00 0.00 ATOM 10 H10 EMI 1 4.839 29.853 13.640 1.00 0.00 ATOM 11 H11 EMI 1 7.514 32.004 16.038 1.00 0.00 ATOM 12 H12 EMI 1 7.951 31.796 13.329 1.00 0.00 ATOM 13 H13 EMI 1 7.967 30.145 13.270 1.00 0.00 ATOM 14 H14 EMI 1 6.890 31.170 12.362 1.00 0.00 ATOM 15 H15 EMI 1 5.214 32.491 18.125 1.00 0.00 ATOM 16 H16 EMI 1 6.495 31.335 18.302 1.00 0.00 ATOM 17 H17 EMI 1 4.834 29.492 18.590 1.00 0.00 ATOM 18 H18 EMI 1 4.337 30.767 19.685 1.00 0.00 ATOM 19 H19 EMI 1 3.486 30.669 18.338 1.00 0.00 ATOM 20 S20 ETS 2 13.817 2.976 33.669 1.00 0.00 ATOM 21 O21 ETS 2 15.031 2.685 34.347 1.00 0.00 ATOM 22 O22 ETS 2 14.005 3.313 32.237 1.00 0.00 ATOM 23 O23 ETS 2 12.775 1.970 33.860 1.00 0.00 ATOM 24 O24 ETS 2 13.303 4.314 34.278 1.00 0.00 ATOM 25 C25 ETS 2 12.361 5.280 33.781 1.00 0.00 ATOM 26 C26 ETS 2 12.277 6.501 34.666 1.00 0.00 ATOM 27 H27 ETS 2 12.582 5.675 32.806 1.00 0.00 ATOM 28 H28 ETS 2 11.377 4.787 33.550 1.00 0.00 ATOM 29 H29 ETS 2 11.686 6.245 35.492 1.00 0.00 ATOM 30 H30 ETS 2 13.256 6.810 34.975 1.00 0.00 ATOM 31 H31 ETS 2 11.856 7.349 34.171 1.00 0.00 ATOM 32 C EMI 3 25.075 29.706 5.816 1.00 0.00 ATOM 33 C2 EMI 3 24.256 29.876 6.894 1.00 0.00 ATOM 34 N3 EMI 3 25.074 30.288 7.940 1.00 0.00 ATOM 35 C4 EMI 3 26.335 30.336 7.464 1.00 0.00 ATOM 36 N5 EMI 3 26.369 29.867 6.216 1.00 0.00 ATOM 37 C6 EMI 3 27.586 29.761 5.460 1.00 0.00 ATOM 38 C7 EMI 3 27.397 29.088 4.106 1.00 0.00 ATOM 39 C8 EMI 3 24.601 30.404 9.351 1.00 0.00 ATOM 40 H9 EMI 3 24.815 29.446 4.790 1.00 0.00 ATOM 41 H10 EMI 3 23.203 29.817 6.920 1.00 0.00 ATOM 42 H11 EMI 3 27.238 30.558 8.074 1.00 0.00 ATOM 43 H12 EMI 3 24.321 29.435 9.759 1.00 0.00 ATOM 44 H13 EMI 3 25.411 30.876 9.880 1.00 0.00 ATOM 45 H14 EMI 3 23.735 31.092 9.515 1.00 0.00 ATOM 46 H15 EMI 3 28.216 29.130 6.169 1.00 0.00 ATOM 47 H16 EMI 3 28.027 30.763 5.434 1.00 0.00 ATOM 48 H17 EMI 3 26.886 29.695 3.344 1.00 0.00 ATOM 49 H18 EMI 3 28.366 28.886 3.715 1.00 0.00 ATOM 50 H19 EMI 3 26.842 28.200 3.880 1.00 0.00 ATOM 51 S20 ETS 4 26.876 17.203 7.791 1.00 0.00 ATOM 52 O21 ETS 4 28.030 16.750 7.061 1.00 0.00 ATOM 53 O22 ETS 4 25.656 16.428 7.528 1.00 0.00 ATOM 54 O23 ETS 4 27.112 17.470 9.202 1.00 0.00 ATOM 55 O24 ETS 4 26.578 18.733 7.129 1.00 0.00 ATOM 56 C25 ETS 4 26.215 18.995 5.843 1.00 0.00 ATOM 57 C26 ETS 4 27.436 19.133 4.921 1.00 0.00 ATOM 58 H27 ETS 4 25.607 18.170 5.486 1.00 0.00 ATOM 59 H28 ETS 4 25.530 19.872 5.774 1.00 0.00 ATOM 60 H29 ETS 4 28.107 19.910 5.179 1.00 0.00 ATOM 61 H30 ETS 4 27.944 18.247 4.832 1.00 0.00 ATOM 62 H31 ETS 4 27.138 19.330 3.927 1.00 0.00 TER ENDMDL snip [ molecules ] ; Compound#mols EMI 2 ETS 2 As I suspected, your molecules are simply out of order. Your topology specifies EMI-EMI-ETS-ETS, but the coordinate file lists the molecules as EMI-ETS-EMI-ETS, hence the mismatch. The Protein [moleculetype] seems superfluous, but would be the appropriate
Re: [gmx-users] grompp Warning: atom name 20 in p2.top and p2.pdb does not match
On 9/22/13 9:32 PM, Nilesh Dhumal wrote: Thanks. I have total 128 EMI and 128 ETS. To find the solution I test for 2 EMI and 2 ETS. How can I define for 128 EMI and 128 ETS ? List 128 EMI consecutively, followed by 128 ETS consecutively, and make a [molecules] directive analogously. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] grompp for minimization: note warning
Dear Justin I did minimization with the newest version of gromacs (4.6.3). But, unfortunately, problem was not solved. Best wishes for you. -- 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] grompp for minimization: note warning
Dear Justin Very thanks for your reply. You said I suspect your Gromacs version is somewhat outdated, as recent versions account for periodicity when making this check. I used 4.5.5 version of gromacs. What version of gromacs is more appropriate for my case. Based on your suggestion, I used -maxwarn option for grompp. Then I used -nt 1 option for mdrun, but this step takes too long and Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=5 Warning: 1-4 interaction between 434 and 407 at distance 3.023 which is larger than the 1-4 table size 2.200 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size step 23: Water molecule starting at atom 10613 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 2122 steps, but did not reach the requested Fmax 1000. Potential Energy = 1.4310875e+05 Maximum force = 2.7179752e+04 on atom 5271 Norm of force = 4.0253470e+02 -- my em.mdp file is as follows: integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 1000.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps= 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom nstlist= 1; Frequency to update the neighbor list and long range forces ns_type= grid; Method to determine neighbor list (simple, grid) rlist= 1.2; Cut-off for making neighbor list (short range forces) coulombtype= PME; Treatment of long range electrostatic interactions rcoulomb= 1.2; Short-range electrostatic cut-off rvdw= 1.2; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions -- gro, edr, trr and lof file were created. I increased emstep from 0.01 to 0.1 and I used constraints = none in mdp file, but result are the same. Is this minimization completely true? Can I use created gro file of this minimization for next step (equilibration)? I am beginner in gromacs, please help me to resolve this problem. Best wishes -- 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] grompp for minimization: note warning
Dear Justin About following warning in grompp using WARNING 1 [file em.mdp]: The sum of the two largest charge group radii (6.940482) is larger than rlist (1.20) You said You probably have molecules split across PBC in the input coordinate file. here's nothing wrong in that case I mention that I used input coordinate file from folloowing web site http://cmb.bio.uni-goettingen.de/cholmembranes.html. Structures in this website were equilibrated 195 ns. Nonetheless, has my input coordinate file problem? -- 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] grompp for minimization: note warning
On 9/16/13 7:37 AM, shahab shariati wrote: Dear Justin About following warning in grompp using WARNING 1 [file em.mdp]: The sum of the two largest charge group radii (6.940482) is larger than rlist (1.20) You said You probably have molecules split across PBC in the input coordinate file. here's nothing wrong in that case I mention that I used input coordinate file from folloowing web site http://cmb.bio.uni-goettingen.de/cholmembranes.html. Structures in this website were equilibrated 195 ns. Nonetheless, has my input coordinate file problem? I have no idea. What file are you using? Visual inspection will make it very obvious whether or not you have broken molecules. My original guess was exactly that - a guess. Based on the supposed size of the group in question, it seemed that it was probably a common membrane issue. Maybe this is or is not the case. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] grompp for minimization: note warning
On 9/16/13 3:06 AM, shahab shariati wrote: Dear Justin Very thanks for your reply. You said I suspect your Gromacs version is somewhat outdated, as recent versions account for periodicity when making this check. I used 4.5.5 version of gromacs. What version of gromacs is more appropriate for my case. When in doubt, always upgrade to the newest version, which is currently 4.6.3. I can't remember when the issue was fixed. Based on your suggestion, I used -maxwarn option for grompp. Then I used -nt 1 option for mdrun, but this step takes too long and Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=5 Warning: 1-4 interaction between 434 and 407 at distance 3.023 which is larger than the 1-4 table size 2.200 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size step 23: Water molecule starting at atom 10613 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 2122 steps, but did not reach the requested Fmax 1000. Potential Energy = 1.4310875e+05 Maximum force = 2.7179752e+04 on atom 5271 Norm of force = 4.0253470e+02 In this case, it is pretty clear that there is actually something wrong with the input coordinates. -- my em.mdp file is as follows: integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 1000.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps= 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom nstlist= 1; Frequency to update the neighbor list and long range forces ns_type= grid; Method to determine neighbor list (simple, grid) rlist= 1.2; Cut-off for making neighbor list (short range forces) coulombtype= PME; Treatment of long range electrostatic interactions rcoulomb= 1.2; Short-range electrostatic cut-off rvdw= 1.2; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions -- gro, edr, trr and lof file were created. I increased emstep from 0.01 to 0.1 and I used constraints = none in mdp file, but result are the same. Increasing emstep does not make sense. If anything, you should be decreasing it to try to take smaller steps and resolve clashes. In any case, the output tells you where the maximum force is. Fire up your favorite visualization software, look at that atom and the things around it, and figure out what is going on. Is this minimization completely true? Can I use created gro file of this minimization for next step (equilibration)? No, the forces are far too high to be useful. Anything you do will simply crash. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] grompp for minimization: note warning
Dear gromacs users My system contains 3 components: DOPC cholesterol lipids + drug + water molecules. In minimization step, when I use grompp -f em.mdp -c system.gro -p topol.top -o em.tpr, I encountered with following note and warning: WARNING 1 [file em.mdp]: The sum of the two largest charge group radii (6.940482) is larger than rlist (1.20) Calculating fourier grid dimensions for X Y Z Using a fourier grid of 72x72x72, spacing 0.111 0.120 0.116 Estimate for the relative computational load of the PME mesh part: 0.62 NOTE 1 [file em.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing --- My em.mdp file is as follows: ; em.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 1000.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps= 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom nstlist= 1; Frequency to update the neighbor list and long range forces ns_type= grid; Method to determine neighbor list (simple, grid) rlist= 1.2; Cut-off for making neighbor list (short range forces) coulombtype= PME; Treatment of long range electrostatic interactions rcoulomb= 1.2; Short-range electrostatic cut-off rvdw= 1.2; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions - I dont like to use -maxwarn option. How to modify parameters in em.mdp file to resolve note an warning. Any help will highly appreciated. Best wishes. -- 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] grompp for minimization: note warning
Dear gromacs users Nember of groups in each of charge groups is less than or equal 3. charge groups in my itp files are as follows: DOPC.itp: [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 CH3* 1 DOPC C1 10.4 15.035 2 CH3* 1 DOPC C2 20.4 15.035 3 CH3* 1 DOPC C3 30.4 15.035 4NL 1 DOPC N4 4 -0.514.0067 5 CH2* 1 DOPC C5 50.3 14.027 6 CH2* 1 DOPC C6 60.4 14.027 7OA 1 DOPCOS7 7 -0.815.9994 8 P 1 DOPC P8 81.730.9738 9OM* 1 DOPCOM9 9 -0.815.9994 10OM* 1 DOPC OM10 10 -0.815.9994 11OA 1 DOPC OS11 11 -0.715.9994 12CH2* 1 DOPCC12 120.4 14.027 13 CH1* 1 DOPCC13 130.3 13.019 14OA 1 DOPC OS14 14 -0.715.9994 15CO* 1 DOPCC15 150.7 12.011 16 O* 1 DOPCO16 16 -0.715.9994 17 CH2* 1 DOPCC17 17 0 14.027 18 CH2* 1 DOPCC18 17 0 14.027 19 CH2* 1 DOPCC19 17 0 14.027 20 CH2* 1 DOPCC20 18 0 14.027 21 CH2* 1 DOPCC21 18 0 14.027 22 CH2* 1 DOPCC22 18 0 14.027 23 CH2* 1 DOPCC23 19 0 14.027 24 C*H1 1 DOPCC24 19 0 13.019 25 C*H1 1 DOPCC25 19 0 13.019 26 CH2* 1 DOPCC26 20 0 14.027 27 CH2* 1 DOPCC27 20 0 14.027 28 CH2* 1 DOPCC28 20 0 14.027 29 CH2* 1 DOPCC29 21 0 14.027 30 CH2* 1 DOPCC30 21 0 14.027 31 CH2* 1 DOPCC31 21 0 15.035 32 CH2* 1 DOPCC32 22 0 14.027 33 CH3* 1 DOPCC33 220.0 15.035 34 CH2* 1 DOPCC34 230.5 14.027 35OA 1 DOPC OS35 24 -0.715.9994 36CO* 1 DOPCC36 250.8 12.011 37 O* 1 DOPCO37 26 -0.615.9994 38 CH2* 1 DOPCC38 27 0 14.027 39 CH2* 1 DOPCC39 27 0 14.027 40 CH2* 1 DOPCC40 27 0 14.027 41 CH2* 1 DOPCC41 28 0 14.027 42 CH2* 1 DOPCC42 28 0 14.027 43 CH2* 1 DOPCC43 28 0 14.027 44 CH2* 1 DOPCC44 29 0 14.027 45 C*H1 1 DOPCC45 29 0 13.019 46 C*H1 1 DOPCC46 29 0 13.019 47 CH2* 1 DOPCC47 30 0 14.027 48 CH2* 1 DOPCC48 30 0 14.027 49 CH2* 1 DOPCC49 30 0 14.027 50 CH2* 1 DOPCC50 31 0 14.027 51 CH2* 1 DOPCC51 31 0 14.027 52 CH2* 1 DOPCC52 31 0 14.027 53 CH2* 1 DOPCC53 32 0 14.027 54 CH3* 1 DOPCC54 32 0 15.035 cholesterol.itp: [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1CH2R61CHOL C110.014.027 2CH2R6 1 CHOLC220.0 14.027 3CH1R6 1 CHOLC330.270 13.019 4CH2R6 1 CHOLC440.0 14.027 5C* 1 CHOLC550.012.011 6C*HR6 1 CHOLC660.0 13.019 7CH2R6 1 CHOLC770.0 14.027 8CH1R61 CHOLC880.013.019 9CH1R6 1 CHOLC990.0 13.019 10CH0*1 CHOLC10100.012.011 11CH2R6 1 CHOLC11110.0 14.027 12CH2R6 1 CHOLC12120.0 14.027 13CH0*1 CHOLC13130.0 12.011 14 CH1R6 1 CHOLC14 14 0.0 13.019 15CH2R51 CHOLC15150.0 14.027 16CH2R5 1 CHOLC16160.0 14.027 17 CH1R5 1
[gmx-users] grompp for minimization: note warning
Dear gromacs users I used -maxwarn option, but after using this command: mdrun -s em.tpr -o em.trr -c em.gro -e em.edr -g em.log I encountered with: Fatal error: There is no domain decomposition for 4 nodes that is compatible with the given box and a minimum cell size of 6.61528 nm Change the number of nodes or mdrun option -rdd Look in the log file for details on the domain decomposition Based on above suggestion, I should use option -rdd with mdrun, but I dont what argument with -rdd? What value is appropriate for -rdd? 0 or other? Best wishes -- 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] grompp for minimization: note warning
On 9/15/13 3:44 AM, shahab shariati wrote: Dear gromacs users My system contains 3 components: DOPC cholesterol lipids + drug + water molecules. In minimization step, when I use grompp -f em.mdp -c system.gro -p topol.top -o em.tpr, I encountered with following note and warning: WARNING 1 [file em.mdp]: The sum of the two largest charge group radii (6.940482) is larger than rlist (1.20) http://www.gromacs.org/Documentation/Errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb You probably have molecules split across PBC in the input coordinate file. There's nothing wrong in that case. Calculating fourier grid dimensions for X Y Z Using a fourier grid of 72x72x72, spacing 0.111 0.120 0.116 Estimate for the relative computational load of the PME mesh part: 0.62 NOTE 1 [file em.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing --- For energy minimization, this doesn't really matter. My em.mdp file is as follows: ; em.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 1000.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps= 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom nstlist= 1; Frequency to update the neighbor list and long range forces ns_type= grid; Method to determine neighbor list (simple, grid) rlist= 1.2; Cut-off for making neighbor list (short range forces) coulombtype= PME; Treatment of long range electrostatic interactions rcoulomb= 1.2; Short-range electrostatic cut-off rvdw= 1.2; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions - I dont like to use -maxwarn option. How to modify parameters in em.mdp file to resolve note an warning. If you do, in fact, have broken molecules in the input coordinates, then -maxwarn is actually OK. I suspect your Gromacs version is somewhat outdated, as recent versions account for periodicity when making this check. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] grompp for minimization: note warning
On 9/15/13 8:17 AM, shahab shariati wrote: Dear gromacs users I used -maxwarn option, but after using this command: mdrun -s em.tpr -o em.trr -c em.gro -e em.edr -g em.log I encountered with: Fatal error: There is no domain decomposition for 4 nodes that is compatible with the given box and a minimum cell size of 6.61528 nm Change the number of nodes or mdrun option -rdd Look in the log file for details on the domain decomposition Based on above suggestion, I should use option -rdd with mdrun, but I dont what argument with -rdd? What value is appropriate for -rdd? 0 or other? Not all systems can be decomposed to run on any arbitrary number of cores/threads. http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm See my previous message for my thoughts on the error grompp gave you, as it relates to this one. Regardless, running with -nt 1 will work and should complete reasonably quickly (EM shouldn't take too long). -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] grompp error
Thanks On Tue, Jun 18, 2013 at 10:44 PM, massimo sandal deviceran...@gmail.comwrote: 2013/6/18 Hasni Arsad hasni.ar...@gmail.com What should i do with this error massage: Google it. Program grompp, VERSION 4.6.2 Source code file: /home/hasni/Bioinformatics/gromacs-4.6.2/src/kernel/grompp.c, line: 563 Fatal error: number of coordinates in coordinate file (solv.gro, 50853) does not match topology (topol.top, 50816) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors __ solv.gro file 16268 1MET N1 3.978 6.462 2.460 1MET H12 3.894 6.415 2.435 1MET H23 4.057 6.411 2.426 1MET H34 3.983 6.470 2.560 .. . . . . 275UNK H2 2869 9.769 6.981 4.477 275UNK N1 2870 9.733 7.084 4.303 275UNK C6 2871 9.725 7.203 4.240 275UNK N6 2872 9.693 7.205 4.110 275UNKH62 2873 9.675 7.119 4.062 275UNKH61 2874 9.686 7.292 4.061 276SOL OW 2875 0.569 1.275 1.165 276SOLHW1 2876 0.476 1.268 1.128 276SOLHW2 2877 0.580 1.364 1.209 277SOL OW 2878 1.555 1.511 0.703 277SOLHW1 2879 1.498 1.495 0.784 277SOLHW2 2880 1.496 1.521 0.623 278SOL OW 2881 1.743 0.618 0.856 278SOLHW1 2882 1.776 0.712 0.856 . . 16267SOL OW50848 4.521 3.149 0.076 16267SOLHW150849 4.437 3.148 0.130 16267SOLHW250850 4.523 3.232 0.020 16268SOL OW50851 7.487 8.525 5.886 16268SOLHW150852 7.586 8.514 5.877 16268SOLHW250853 7.447 8.439 5.918 topol.top file [ molecules ] ; Compound#mols Protein_chain_X 1 UNK1 SOL 15993 On Tue, Jun 18, 2013 at 4:36 PM, Mark Abraham mark.j.abra...@gmail.com wrote: GROMACS is not yet magic. You used an atom type not found in your force field. Over to you. :-) Mark On Jun 18, 2013 5:23 AM, Hasni Arsad hasni.ar...@gmail.com wrote: Hi, I got this error massage when execute this command- grompp -f em.mdp -c solvated.pdb -p topol.top Program grompp, VERSION 4.6.2 Source code file: /gromacs-4.6.2/src/kernel/toppush.c, line: 1336 Fatal error: Atomtype NPYL not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors comment please! -- 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 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 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 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 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] grompp error
Thanks, Finally I managed to run MD of protein-ligand complex after a few trial of tutorial On Tue, Jun 18, 2013 at 5:06 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Please keep GROMACS usage questions on the gmx-users mailing list. Nobody here is a private tutor :-) The error messages you are getting are self-explanatory. You need to think about why they are arising. Perhaps do some tutorials to get a feel for normal workflows, and how best to modify them to suit your needs. Mark On Tue, Jun 18, 2013 at 10:57 AM, Hasni Arsad hasni.ar...@gmail.com wrote: -- Forwarded message -- From: Hasni Arsad hasni.ar...@gmail.com Date: Tue, Jun 18, 2013 at 4:55 PM Subject: Re: [gmx-users] grompp error To: Discussion list for GROMACS users gmx-users@gromacs.org What should i do with this error massage: Program grompp, VERSION 4.6.2 Source code file: /home/hasni/Bioinformatics/gromacs-4.6.2/src/kernel/grompp.c, line: 563 Fatal error: number of coordinates in coordinate file (solv.gro, 16268) does not match topology (topol.top, 50816) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors __ Attach is my topol.top and solv.gro. On Tue, Jun 18, 2013 at 4:36 PM, Mark Abraham mark.j.abra...@gmail.com wrote: GROMACS is not yet magic. You used an atom type not found in your force field. Over to you. :-) Mark On Jun 18, 2013 5:23 AM, Hasni Arsad hasni.ar...@gmail.com wrote: Hi, I got this error massage when execute this command- grompp -f em.mdp -c solvated.pdb -p topol.top Program grompp, VERSION 4.6.2 Source code file: /gromacs-4.6.2/src/kernel/toppush.c, line: 1336 Fatal error: Atomtype NPYL not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors comment please! -- 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 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 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 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] grompp error
GROMACS is not yet magic. You used an atom type not found in your force field. Over to you. :-) Mark On Jun 18, 2013 5:23 AM, Hasni Arsad hasni.ar...@gmail.com wrote: Hi, I got this error massage when execute this command- grompp -f em.mdp -c solvated.pdb -p topol.top Program grompp, VERSION 4.6.2 Source code file: /gromacs-4.6.2/src/kernel/toppush.c, line: 1336 Fatal error: Atomtype NPYL not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors comment please! -- 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 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] grompp error
Please keep GROMACS usage questions on the gmx-users mailing list. Nobody here is a private tutor :-) The error messages you are getting are self-explanatory. You need to think about why they are arising. Perhaps do some tutorials to get a feel for normal workflows, and how best to modify them to suit your needs. Mark On Tue, Jun 18, 2013 at 10:57 AM, Hasni Arsad hasni.ar...@gmail.com wrote: -- Forwarded message -- From: Hasni Arsad hasni.ar...@gmail.com Date: Tue, Jun 18, 2013 at 4:55 PM Subject: Re: [gmx-users] grompp error To: Discussion list for GROMACS users gmx-users@gromacs.org What should i do with this error massage: Program grompp, VERSION 4.6.2 Source code file: /home/hasni/Bioinformatics/gromacs-4.6.2/src/kernel/grompp.c, line: 563 Fatal error: number of coordinates in coordinate file (solv.gro, 16268) does not match topology (topol.top, 50816) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors __ Attach is my topol.top and solv.gro. On Tue, Jun 18, 2013 at 4:36 PM, Mark Abraham mark.j.abra...@gmail.comwrote: GROMACS is not yet magic. You used an atom type not found in your force field. Over to you. :-) Mark On Jun 18, 2013 5:23 AM, Hasni Arsad hasni.ar...@gmail.com wrote: Hi, I got this error massage when execute this command- grompp -f em.mdp -c solvated.pdb -p topol.top Program grompp, VERSION 4.6.2 Source code file: /gromacs-4.6.2/src/kernel/toppush.c, line: 1336 Fatal error: Atomtype NPYL not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors comment please! -- 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 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 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] grompp error
What should i do with this error massage: Program grompp, VERSION 4.6.2 Source code file: /home/hasni/Bioinformatics/gromacs-4.6.2/src/kernel/grompp.c, line: 563 Fatal error: number of coordinates in coordinate file (solv.gro, 50853) does not match topology (topol.top, 50816) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors __ solv.gro file 16268 1MET N1 3.978 6.462 2.460 1MET H12 3.894 6.415 2.435 1MET H23 4.057 6.411 2.426 1MET H34 3.983 6.470 2.560 .. . . . . 275UNK H2 2869 9.769 6.981 4.477 275UNK N1 2870 9.733 7.084 4.303 275UNK C6 2871 9.725 7.203 4.240 275UNK N6 2872 9.693 7.205 4.110 275UNKH62 2873 9.675 7.119 4.062 275UNKH61 2874 9.686 7.292 4.061 276SOL OW 2875 0.569 1.275 1.165 276SOLHW1 2876 0.476 1.268 1.128 276SOLHW2 2877 0.580 1.364 1.209 277SOL OW 2878 1.555 1.511 0.703 277SOLHW1 2879 1.498 1.495 0.784 277SOLHW2 2880 1.496 1.521 0.623 278SOL OW 2881 1.743 0.618 0.856 278SOLHW1 2882 1.776 0.712 0.856 . . 16267SOL OW50848 4.521 3.149 0.076 16267SOLHW150849 4.437 3.148 0.130 16267SOLHW250850 4.523 3.232 0.020 16268SOL OW50851 7.487 8.525 5.886 16268SOLHW150852 7.586 8.514 5.877 16268SOLHW250853 7.447 8.439 5.918 topol.top file [ molecules ] ; Compound#mols Protein_chain_X 1 UNK1 SOL 15993 On Tue, Jun 18, 2013 at 4:36 PM, Mark Abraham mark.j.abra...@gmail.comwrote: GROMACS is not yet magic. You used an atom type not found in your force field. Over to you. :-) Mark On Jun 18, 2013 5:23 AM, Hasni Arsad hasni.ar...@gmail.com wrote: Hi, I got this error massage when execute this command- grompp -f em.mdp -c solvated.pdb -p topol.top Program grompp, VERSION 4.6.2 Source code file: /gromacs-4.6.2/src/kernel/toppush.c, line: 1336 Fatal error: Atomtype NPYL not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors comment please! -- 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 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 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] grompp error
2013/6/18 Hasni Arsad hasni.ar...@gmail.com What should i do with this error massage: Google it. Program grompp, VERSION 4.6.2 Source code file: /home/hasni/Bioinformatics/gromacs-4.6.2/src/kernel/grompp.c, line: 563 Fatal error: number of coordinates in coordinate file (solv.gro, 50853) does not match topology (topol.top, 50816) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors __ solv.gro file 16268 1MET N1 3.978 6.462 2.460 1MET H12 3.894 6.415 2.435 1MET H23 4.057 6.411 2.426 1MET H34 3.983 6.470 2.560 .. . . . . 275UNK H2 2869 9.769 6.981 4.477 275UNK N1 2870 9.733 7.084 4.303 275UNK C6 2871 9.725 7.203 4.240 275UNK N6 2872 9.693 7.205 4.110 275UNKH62 2873 9.675 7.119 4.062 275UNKH61 2874 9.686 7.292 4.061 276SOL OW 2875 0.569 1.275 1.165 276SOLHW1 2876 0.476 1.268 1.128 276SOLHW2 2877 0.580 1.364 1.209 277SOL OW 2878 1.555 1.511 0.703 277SOLHW1 2879 1.498 1.495 0.784 277SOLHW2 2880 1.496 1.521 0.623 278SOL OW 2881 1.743 0.618 0.856 278SOLHW1 2882 1.776 0.712 0.856 . . 16267SOL OW50848 4.521 3.149 0.076 16267SOLHW150849 4.437 3.148 0.130 16267SOLHW250850 4.523 3.232 0.020 16268SOL OW50851 7.487 8.525 5.886 16268SOLHW150852 7.586 8.514 5.877 16268SOLHW250853 7.447 8.439 5.918 topol.top file [ molecules ] ; Compound#mols Protein_chain_X 1 UNK1 SOL 15993 On Tue, Jun 18, 2013 at 4:36 PM, Mark Abraham mark.j.abra...@gmail.com wrote: GROMACS is not yet magic. You used an atom type not found in your force field. Over to you. :-) Mark On Jun 18, 2013 5:23 AM, Hasni Arsad hasni.ar...@gmail.com wrote: Hi, I got this error massage when execute this command- grompp -f em.mdp -c solvated.pdb -p topol.top Program grompp, VERSION 4.6.2 Source code file: /gromacs-4.6.2/src/kernel/toppush.c, line: 1336 Fatal error: Atomtype NPYL not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors comment please! -- 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 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 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 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] grompp error
Hi, I got this error massage when execute this command- grompp -f em.mdp -c solvated.pdb -p topol.top Program grompp, VERSION 4.6.2 Source code file: /gromacs-4.6.2/src/kernel/toppush.c, line: 1336 Fatal error: Atomtype NPYL not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors comment please! -- 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] grompp error
Hello all, I am new user of gromacs. I am doing Tutorial 1. When I run grompp, following problem occurred:Program grompp, VERSION 4.5.3Source code file: toppush.c, line: 1987Fatal error:No such moleculetype CL-For more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/ErrorsHow can I solve this?Mijiddorj -- View this message in context: http://gromacs.5086.n6.nabble.com/grompp-error-tp5004198.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] grompp error
On 1/2/13 10:01 AM, Mijiddorj wrote: Hello all, I am new user of gromacs. I am doing Tutorial 1. When I run grompp, following problem occurred:Program grompp, VERSION 4.5.3Source code file: toppush.c, line: 1987Fatal error:No such moleculetype CL-For more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/ErrorsHow can I solve this?Mijiddorj You named your ions wrong. Please read the help information from genion -h: The ion molecule type, residue and atom names in all force fields are the capitalized element names without sign. This molecule name should be given with -pname or -nname, and the [molecules] section of your topology updated accordingly, either by hand or with -p. Do not use an atom name instead! Note that, if you are referring to my Tutorial 1 on lysozyme, the naming issue is explained and the genion command should be copied verbatim, as I do not use any +/- signs in the -pname or -nname options. -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] grompp error
On 10/22/12 8:46 PM, Nur Syafiqah Abdul Ghani wrote: Dear All, Right now i want to do another simulation which is water and co-solvent,HFIP. I get the small compound file from http://compbio.biosci.uq.edu.au/atb/download.py?molid=6187#files I need to used the all atom one and the force field that i used is gromos96. Right now i'm done packing the HFIP and the water by using packmol and change all the pdb file into gro file. Therefore I want to minimize them by using the command like below: grompp -f em1.mdp -c mixture.gro -p topol.top -o minimize.tpr -v and the error that coming out is : Fatal error: Syntax error - File solvent.itp, line 1 Last line read: '[ atoms ]' Invalid order for directive atoms So, I already checked the problem by gedit the solvent.itp.Here is my itp file : The first part of an .itp file needs to be a [moleculetype] directive that names the molecule and defines its number of exclusions. [ atoms ] ; nr type resnr resid atom cgnr chargemasstotal_charge 1 CH01hfi C110.384 12.0110 2 F1hfi F11 -0.128 18.9984 3 F1hfi F21 -0.128 18.9984 4 F1hfi F31 -0.128 18.9984 ; 0.000 . 9 CH01hfi C330.384 12.0110 10 F1hfi F43 -0.128 18.9984 .. ; total charge of the molecule: 0.000 [ bonds ] ; ai aj funct c0 c1 122 0.1360 7.2300e+06 132 0.1360 4.7700e+06 ... 9 112 0.1360 4.7700e+06 9 122 0.1360 7.2300e+06 [ pairs ] ; ai aj funct ; all 1-4 pairs but the ones excluded in GROMOS itp 181 1 101 1 111 1 121 261 ... 681 6 101 6 111 ... 7 111 7 121 891 [ angles ] ; ai aj ak funct angle fc 2132107.60 507.00 2142107.60 507.00 2152111.40 532.00 3142107.60 507.00 .. 59 102111.40 532.00 59 112111.40 532.00 59 122109.50 618.00 .. 119 122107.60 507.00 [ dihedrals ] ; GROMOS improper dihedrals ; ai aj ak al funct angle fc [ dihedrals ] ; ai aj ak al functph0 cp mult 21591 0.00 3.773 [ exclusions ] ; ai aj funct ; GROMOS 1-4 exclusions and the topology file is : The first thing you need to #include is the parent force field, from which bonded and nonbonded parameters are taken. -Justin ; Include topology for solvent #include solvent.itp ; ; Include water topology #include gromos53a6.ff/spc.itp ; #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; [ system ] ; Name solvent in water box ; ; [ molecules ] ; Compound #mols hfi ... Is thereany typing error that i seem cant see? I already compare with other problem but seems that I'm lost. Thanks in advance, Best Regards, Nur Syafiqah Abdul Ghani, Theoretical and Computational Chemistry Laboratory, Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 Serdang, Selangor. 013-7188131 alternative email : syafiqahabdulgh...@gmail.com -- 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] grompp errors..
On 9/29/12 12:55 PM, Ali Alizadeh wrote: Dear All users I have a system with 3 layers, when i run grompp program, encounter with this error. First and 3th layer is the same, and middle layer is water. what's this error about? grompp is looking for some group called 1 (the number one) but it can't find such a group. The error suggests that you use a custom index group. In the absence of an .mdp file and a list of the index groups that you're trying to use, we can't really guess what's supposed to be happening. and i have another question about make_ndx, How to make index the same atoms with different res number in .gro file? Type help at the make_ndx prompt to see examples. If you need specific help with a specific task, ask a more specific question :) -Justin .. Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'cpp' Ignoring obsolete mdp entry 'nstcheckpoint' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.7# Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Ion' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Ion2' turning all bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning all bonds into constraints... Analysing residue names: There are: 1183Ion residues There are: 1830 Water residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group System is 23990.00 --- Program grompp, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/kernel/readir.c, line: 1320 Fatal error: Group 1 not found in index file. Group names must match either [moleculetype] names or custom index group names,in which case you must supply an index file to the '-n' option of grompp. -- 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] grompp warnings Overriding atomtype ...
On 9/22/12 10:04 PM, Leandro Bortot wrote: Dear all, I am trying to do a glycoprotein simulation with GROMACS using the AMBER99SB-ILDN forcefield together with GLYCAM06. After constructing my glycoprotein grompp gives the following warning for most of the atomtypes defined in the .itp file with the glycoprotein parameters: WARNING 23 [file glycoprot.itp, line 27]: Overriding atomtype CC Is this supposed to be this way? Because there are new definitions of atomtypes which are not used in the carbohydrate nor in the glycosylated residue, I suppose that these parameters are really meant to override the default ones since they are only necessary for water and ions. Am I right? An atom type of CC is certainly nothing to do with water and ions - it's a carbon atom type. Above you say the warnings are generated from the glycoprotein topology. That's your problem. The parameters introduced here are fighting those built into the AMBER99SB-ILDN force field. Atom types are case-sensitive, so if you truly need new parameters then you can change the case and they will not override. If the atom type parameters are duplicates of existing ones, then you can ignore the warning. -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
[gmx-users] grompp in KALP15-DPPC
Hi, I am doing the simulation of KALP15 in DPPC following the Justin's tutorial. For the step of solvation I ran this command: # genbox -cp system.gro -cs spc216.gro -o system_solv.gro -p topol.top The output of this step is as here: Reading solute configuration frame t= 1.000 Containing 17503 atoms in 3800 residues Initialising van der waals distances... 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. Reading solvent configuration 216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984 solvent configuration contains 648 atoms in 216 residues Initialising van der waals distances... Will generate new solvent configuration of 4x4x4 boxes Generating configuration Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 13824 residues Calculating Overlap... box_margin = 0.315 Removed 10608 atoms that were outside the box Neighborsearching with a cut-off of 1.125 Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE Cut-off's: NS: 1.125 Coulomb: 1.125 LJ: 1.125 System total charge: 0.000 Grid: 18 x 18 x 18 cells Successfully made neighbourlist nri = 152829, nrj = 41861902 Checking Protein-Solvent overlap: tested 3204927 pairs, removed 30048 atoms. Checking Solvent-Solvent overlap: tested 17610 pairs, removed 60 atoms. Added 252 molecules Generated solvent containing 756 atoms in 252 residues Writing generated configuration to system_solv.gro Back Off! I just backed up system_solv.gro to ./#system_solv.gro.3# frame t= 1.000 Output configuration contains 18259 atoms in 4052 residues Volume : 272.811 (nm^3) Density : 947.87 (g/l) Number of SOL molecules: 3907 Processing topology Removing line #929 'SOL 533' from topology file (topol.top) Then running grompp for the next step ( neutralization ) grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr But the error is: Fatal error: number of coordinates in coordinate file (system_solv.gro, 18259) does not match topology (topol.top, 18159) For more information and tips for troubleshooting, please check the GROMACS Would you pleas help me? Do I need to modify the .top file before running grompp? Thanks for your suggestions in advance. Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] grompp in KALP15-DPPC
On 8/25/12 12:26 PM, Shima Arasteh wrote: Hi, I am doing the simulation of KALP15 in DPPC following the Justin's tutorial. For the step of solvation I ran this command: # genbox -cp system.gro -cs spc216.gro -o system_solv.gro -p topol.top The output of this step is as here: Reading solute configuration frame t= 1.000 Containing 17503 atoms in 3800 residues Initialising van der waals distances... 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. Reading solvent configuration 216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984 solvent configuration contains 648 atoms in 216 residues Initialising van der waals distances... Will generate new solvent configuration of 4x4x4 boxes Generating configuration Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 13824 residues Calculating Overlap... box_margin = 0.315 Removed 10608 atoms that were outside the box Neighborsearching with a cut-off of 1.125 Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE Cut-off's: NS: 1.125 Coulomb: 1.125 LJ: 1.125 System total charge: 0.000 Grid: 18 x 18 x 18 cells Successfully made neighbourlist nri = 152829, nrj = 41861902 Checking Protein-Solvent overlap: tested 3204927 pairs, removed 30048 atoms. Checking Solvent-Solvent overlap: tested 17610 pairs, removed 60 atoms. Added 252 molecules Generated solvent containing 756 atoms in 252 residues Writing generated configuration to system_solv.gro Back Off! I just backed up system_solv.gro to ./#system_solv.gro.3# frame t= 1.000 Output configuration contains 18259 atoms in 4052 residues Volume : 272.811 (nm^3) Density: 947.87 (g/l) Number of SOL molecules: 3907 Processing topology Removing line #929 'SOL 533' from topology file (topol.top) Then running grompp for the next step ( neutralization ) grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr But the error is: Fatal error: number of coordinates in coordinate file (system_solv.gro, 18259) does not match topology (topol.top, 18159) For more information and tips for troubleshooting, please check the GROMACS Would you pleas help me? Do I need to modify the .top file before running grompp? Well, something doesn't match, so yes. But at the same time, if you're properly maintained the topology thus far, then you shouldn't have to. A difference of 100 atoms suggests there are 2 extra DPPC molecules in the coordinate file relative to the topology. I have no idea how you would have produced such a mismatch though. -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 * Only plain text messages are allowed! * 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] grompp in KALP15-DPPC
The number of DPPC molecules were 126. I changed it to 128 in topol.top, then the grompp didn't give me any fatal error. I had changed the number of DPPC in top file in last step when the inflateGRO reporst that 2 DPPC were removed. Now, 128 DPPC is acceptable! What does it mean? Is it sensible? Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, August 25, 2012 8:59 PM Subject: Re: [gmx-users] grompp in KALP15-DPPC On 8/25/12 12:26 PM, Shima Arasteh wrote: Hi, I am doing the simulation of KALP15 in DPPC following the Justin's tutorial. For the step of solvation I ran this command: # genbox -cp system.gro -cs spc216.gro -o system_solv.gro -p topol.top The output of this step is as here: Reading solute configuration frame t= 1.000 Containing 17503 atoms in 3800 residues Initialising van der waals distances... 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. Reading solvent configuration 216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984 solvent configuration contains 648 atoms in 216 residues Initialising van der waals distances... Will generate new solvent configuration of 4x4x4 boxes Generating configuration Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 13824 residues Calculating Overlap... box_margin = 0.315 Removed 10608 atoms that were outside the box Neighborsearching with a cut-off of 1.125 Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE Cut-off's: NS: 1.125 Coulomb: 1.125 LJ: 1.125 System total charge: 0.000 Grid: 18 x 18 x 18 cells Successfully made neighbourlist nri = 152829, nrj = 41861902 Checking Protein-Solvent overlap: tested 3204927 pairs, removed 30048 atoms. Checking Solvent-Solvent overlap: tested 17610 pairs, removed 60 atoms. Added 252 molecules Generated solvent containing 756 atoms in 252 residues Writing generated configuration to system_solv.gro Back Off! I just backed up system_solv.gro to ./#system_solv.gro.3# frame t= 1.000 Output configuration contains 18259 atoms in 4052 residues Volume : 272.811 (nm^3) Density : 947.87 (g/l) Number of SOL molecules: 3907 Processing topology Removing line #929 'SOL 533' from topology file (topol.top) Then running grompp for the next step ( neutralization ) grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr But the error is: Fatal error: number of coordinates in coordinate file (system_solv.gro, 18259) does not match topology (topol.top, 18159) For more information and tips for troubleshooting, please check the GROMACS Would you pleas help me? Do I need to modify the .top file before running grompp? Well, something doesn't match, so yes. But at the same time, if you're properly maintained the topology thus far, then you shouldn't have to. A difference of 100 atoms suggests there are 2 extra DPPC molecules in the coordinate file relative to the topology. I have no idea how you would have produced such a mismatch though. -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 * Only plain text messages are allowed! * 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] grompp in KALP15-DPPC
On 8/25/12 12:41 PM, Shima Arasteh wrote: The number of DPPC molecules were 126. I changed it to 128 in topol.top, then the grompp didn't give me any fatal error. I had changed the number of DPPC in top file in last step when the inflateGRO reporst that 2 DPPC were removed. Now, 128 DPPC is acceptable! What does it mean? Is it sensible? Not in the least. You should make one change to the [molecules] (when InflateGRO deletes lipids) and never manually adjust it again. You need to check your work, because I suspect you're using the wrong files (either topology or coordinates) because suddenly there's a mismatch that shouldn't be happening. You can always check what's in your coordinate file with grep to do counting, e.g.: grep -c P8 (name of your coordinate file) That will tell you the number of DPPC lipids. Likewise, you can count water molecules (another common source of error) with: grep -c OW (name of your coordinate file) If your coordinate file somehow has 128 DPPC again, then you're using the wrong file. Once deleted, they don't get added back. -Justin Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, August 25, 2012 8:59 PM Subject: Re: [gmx-users] grompp in KALP15-DPPC On 8/25/12 12:26 PM, Shima Arasteh wrote: Hi, I am doing the simulation of KALP15 in DPPC following the Justin's tutorial. For the step of solvation I ran this command: # genbox -cp system.gro -cs spc216.gro -o system_solv.gro -p topol.top The output of this step is as here: Reading solute configuration frame t= 1.000 Containing 17503 atoms in 3800 residues Initialising van der waals distances... 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. Reading solvent configuration 216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984 solvent configuration contains 648 atoms in 216 residues Initialising van der waals distances... Will generate new solvent configuration of 4x4x4 boxes Generating configuration Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 13824 residues Calculating Overlap... box_margin = 0.315 Removed 10608 atoms that were outside the box Neighborsearching with a cut-off of 1.125 Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE Cut-off's: NS: 1.125 Coulomb: 1.125 LJ: 1.125 System total charge: 0.000 Grid: 18 x 18 x 18 cells Successfully made neighbourlist nri = 152829, nrj = 41861902 Checking Protein-Solvent overlap: tested 3204927 pairs, removed 30048 atoms. Checking Solvent-Solvent overlap: tested 17610 pairs, removed 60 atoms. Added 252 molecules Generated solvent containing 756 atoms in 252 residues Writing generated configuration to system_solv.gro Back Off! I just backed up system_solv.gro to ./#system_solv.gro.3# frame t= 1.000 Output configuration contains 18259 atoms in 4052 residues Volume : 272.811 (nm^3) Density: 947.87 (g/l) Number of SOL molecules: 3907 Processing topology Removing line #929 'SOL 533' from topology file (topol.top) Then running grompp for the next step ( neutralization ) grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr But the error is: Fatal error: number of coordinates in coordinate file (system_solv.gro, 18259) does not match topology (topol.top, 18159) For more information and tips for troubleshooting, please check the GROMACS Would you pleas help me? Do I need to modify the .top file before running grompp? Well, something doesn't match, so yes. But at the same time, if you're properly maintained the topology thus far, then you shouldn't have to. A difference of 100 atoms suggests there are 2 extra DPPC molecules in the coordinate file relative to the topology. I have no idea how you would have produced such a mismatch though. -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 * Only plain text messages are allowed! * 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] grompp in KALP15-DPPC
Thanks for your reply. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, August 25, 2012 9:16 PM Subject: Re: [gmx-users] grompp in KALP15-DPPC On 8/25/12 12:41 PM, Shima Arasteh wrote: The number of DPPC molecules were 126. I changed it to 128 in topol.top, then the grompp didn't give me any fatal error. I had changed the number of DPPC in top file in last step when the inflateGRO reporst that 2 DPPC were removed. Now, 128 DPPC is acceptable! What does it mean? Is it sensible? Not in the least. You should make one change to the [molecules] (when InflateGRO deletes lipids) and never manually adjust it again. You need to check your work, because I suspect you're using the wrong files (either topology or coordinates) because suddenly there's a mismatch that shouldn't be happening. You can always check what's in your coordinate file with grep to do counting, e.g.: grep -c P8 (name of your coordinate file) That will tell you the number of DPPC lipids. Likewise, you can count water molecules (another common source of error) with: grep -c OW (name of your coordinate file) If your coordinate file somehow has 128 DPPC again, then you're using the wrong file. Once deleted, they don't get added back. -Justin Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, August 25, 2012 8:59 PM Subject: Re: [gmx-users] grompp in KALP15-DPPC On 8/25/12 12:26 PM, Shima Arasteh wrote: Hi, I am doing the simulation of KALP15 in DPPC following the Justin's tutorial. For the step of solvation I ran this command: # genbox -cp system.gro -cs spc216.gro -o system_solv.gro -p topol.top The output of this step is as here: Reading solute configuration frame t= 1.000 Containing 17503 atoms in 3800 residues Initialising van der waals distances... 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. Reading solvent configuration 216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984 solvent configuration contains 648 atoms in 216 residues Initialising van der waals distances... Will generate new solvent configuration of 4x4x4 boxes Generating configuration Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 13824 residues Calculating Overlap... box_margin = 0.315 Removed 10608 atoms that were outside the box Neighborsearching with a cut-off of 1.125 Table routines are used for coulomb: FALSE Table routines are used for vdw: FALSE Cut-off's: NS: 1.125 Coulomb: 1.125 LJ: 1.125 System total charge: 0.000 Grid: 18 x 18 x 18 cells Successfully made neighbourlist nri = 152829, nrj = 41861902 Checking Protein-Solvent overlap: tested 3204927 pairs, removed 30048 atoms. Checking Solvent-Solvent overlap: tested 17610 pairs, removed 60 atoms. Added 252 molecules Generated solvent containing 756 atoms in 252 residues Writing generated configuration to system_solv.gro Back Off! I just backed up system_solv.gro to ./#system_solv.gro.3# frame t= 1.000 Output configuration contains 18259 atoms in 4052 residues Volume : 272.811 (nm^3) Density : 947.87 (g/l) Number of SOL molecules: 3907 Processing topology Removing line #929 'SOL 533' from topology file (topol.top) Then running grompp for the next step ( neutralization ) grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr But the error is: Fatal error: number of coordinates in coordinate file (system_solv.gro, 18259) does not match topology (topol.top, 18159) For more information and tips for troubleshooting, please check the GROMACS Would you pleas help me? Do I need to modify the .top file before running grompp? Well, something doesn't match, so yes. But at the same time, if you're properly maintained the topology thus far, then you shouldn't have to. A difference of 100 atoms suggests there are 2 extra DPPC molecules in the coordinate file relative to the topology. I have no idea how you would have produced such a mismatch though. -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 list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
[gmx-users] GROMPP replaces lipid atom coordinates with these of water molecules
Hello, I have been running a simple simulation where I replace 150 water molecules in a waterbox with a lipid called DPC to create micelles. This simulation is working fine and I'm getting decent micelles fairly quickly. I am now trying to do the same, but with a small peptide in the simulation box. I think that grompp is using water molecules coordinates to locate the DPC, making non-sensical molecules. Why is grompp doing this in the simulation with the peptide and not without is what stomps me. Here follow more details about my system and errors: A PDB of this atomic mess can be found here: http://www.cs.dal.ca/~cblouin/gromacs/gromppout.pdb I've been working on this for a while now, with no success. Can anyone point me in the right direction? Thanks, Christian -- Here are the command lines that I use: pdb2gmx -f 2LOU.pdb -o protein.gro -i ./include.itp -p protein.top -ignh editconf -f protein.gro -o protein-PBC.gro -bt dodecahedron -d 1.0 genbox -cp protein-PBC.gro -cs spc216.gro -ci dpc -nmol 150 -p protein.top -o protein-water.gro python edittop.py (this python script adjust the protein.top file for the right count of DPC and adds the include statement for DPC). grompp -f minim.mdp -c protein-water.gro -p protein.top -o protein-water.tpr -maxwarn 4 The last grompp command generates the following warning: Warning: atom name 665 in protein.top and protein-water.gro does not match (OW - C1) Warning: atom name 666 in protein.top and protein-water.gro does not match (HW1 - C2) Warning: atom name 667 in protein.top and protein-water.gro does not match (HW2 - C3) ... WARNING 1 [file protein.top, line 4194]: 6900 non-matching atom names atom names from protein.top will be used atom names from protein-water.gro will be ignored If I extract a PDB from the tpr file, the system looks fine except for all of the DPC atoms are now crammed into a rectangular box at the edge of my PBC. In fact, it looks like the coordinates used for the DPC molecules are these of water molecules that got reassigned to the lipids residues. The topology and gro file (if this helps): http://www.cs.dal.ca/~cblouin/gromacs/protein.top http://www.cs.dal.ca/~cblouin/gromacs/protein-water.gro -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] GROMPP replaces lipid atom coordinates with these of water molecules
On 7/23/12 9:54 AM, Christian Blouin wrote: Hello, I have been running a simple simulation where I replace 150 water molecules in a waterbox with a lipid called DPC to create micelles. This simulation is working fine and I'm getting decent micelles fairly quickly. I am now trying to do the same, but with a small peptide in the simulation box. I think that grompp is using water molecules coordinates to locate the DPC, making non-sensical molecules. Why is grompp doing this in the simulation with the peptide and not without is what stomps me. Here follow more details about my system and errors: A PDB of this atomic mess can be found here: http://www.cs.dal.ca/~cblouin/gromacs/gromppout.pdb I've been working on this for a while now, with no success. Can anyone point me in the right direction? Thanks, Christian -- Here are the command lines that I use: pdb2gmx -f 2LOU.pdb -o protein.gro -i ./include.itp -p protein.top -ignh editconf -f protein.gro -o protein-PBC.gro -bt dodecahedron -d 1.0 genbox -cp protein-PBC.gro -cs spc216.gro -ci dpc -nmol 150 -p protein.top -o protein-water.gro python edittop.py (this python script adjust the protein.top file for the right count of DPC and adds the include statement for DPC). grompp -f minim.mdp -c protein-water.gro -p protein.top -o protein-water.tpr -maxwarn 4 The last grompp command generates the following warning: Warning: atom name 665 in protein.top and protein-water.gro does not match (OW - C1) Warning: atom name 666 in protein.top and protein-water.gro does not match (HW1 - C2) Warning: atom name 667 in protein.top and protein-water.gro does not match (HW2 - C3) ... WARNING 1 [file protein.top, line 4194]: 6900 non-matching atom names atom names from protein.top will be used atom names from protein-water.gro will be ignored This is the problem. The order of the [molecules] directive must match that of the coordinate file. If it does not, grompp does precisely what you're seeing - it maps coordinate and topology information incorrectly, causing the rearrangement you're seeing. -Justin If I extract a PDB from the tpr file, the system looks fine except for all of the DPC atoms are now crammed into a rectangular box at the edge of my PBC. In fact, it looks like the coordinates used for the DPC molecules are these of water molecules that got reassigned to the lipids residues. The topology and gro file (if this helps): http://www.cs.dal.ca/~cblouin/gromacs/protein.top http://www.cs.dal.ca/~cblouin/gromacs/protein-water.gro -- 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 * Only plain text messages are allowed! * 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] grompp error - incorrect number of parameters
On 17/05/2012 11:47 PM, Lara Bunte wrote: Hello After grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr I got the error: Incorrect number of parameters - found 2, expected 4 or 4 for U-B. I thought that this could be an inconsistency be declaring the functions, but in my topology I have function 4 (for improper dihedrals): Out of topol.top [ dihedrals ] ; aiajakal functc0c1c2 c3 1 8 6 4 4180 100 And in my .rtp file in the CHARMM27 force field folder I have: Out of .rtp file ; bonds angles dihedrals impropers 1 5 44 There's no aminoacids.rtp file for CHARMM27 that has ever looked like this. Any that did is not CHARMM27. Mark and in my ffbonded.itp file I have: [ dihedraltypes ] ; i j k l funcq0 cq ON1 NN3A CN1A NN2U 4 180 100 So in alle three files, ffbonded.itp, topol.top and the .rtp parametrization file I have the function 4 for the improper dihedrals. What is the problem? Thanks for helping me Greetings Lara -- 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] grompp error - incorrect number of parameters
Hello After grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr I got the error: Incorrect number of parameters - found 2, expected 4 or 4 for U-B. I thought that this could be an inconsistency be declaring the functions, but in my topology I have function 4 (for improper dihedrals): Out of topol.top [ dihedrals ] ; ai aj ak al funct c0 c1 c2 c3 1 8 6 4 4 180 100 And in my .rtp file in the CHARMM27 force field folder I have: Out of .rtp file ; bonds angles dihedrals impropers 1 5 4 4 and in my ffbonded.itp file I have: [ dihedraltypes ] ; i j k l func q0 cq ON1 NN3A CN1A NN2U 4 180 100 So in alle three files, ffbonded.itp, topol.top and the .rtp parametrization file I have the function 4 for the improper dihedrals. What is the problem? Thanks for helping me Greetings Lara -- 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] grompp error - incorrect number of parameters
On 5/17/12 9:47 AM, Lara Bunte wrote: Hello After grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr I got the error: Incorrect number of parameters - found 2, expected 4 or 4 for U-B. I thought that this could be an inconsistency be declaring the functions, but in my topology I have function 4 (for improper dihedrals): Out of topol.top [ dihedrals ] ; aiajakal functc0c1c2 c3 1 8 6 4 4180 100 And in my .rtp file in the CHARMM27 force field folder I have: Out of .rtp file ; bonds angles dihedrals impropers 1 5 44 and in my ffbonded.itp file I have: [ dihedraltypes ] ; i j k l funcq0 cq ON1 NN3A CN1A NN2U 4 180 100 So in alle three files, ffbonded.itp, topol.top and the .rtp parametrization file I have the function 4 for the improper dihedrals. What is the problem? The U-B function type is the Urey-Bradley angle potential. It is unrelated to dihedrals. See the [angletypes] directive of ffbonded.itp and the manual for the proper format of U-B parameters. -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
[gmx-users] grompp Unkown bond_atomtype C2
Hi After: pdb2gmx -f mymol.pdb -water tip3p editconf -f conf.gro -bt dodecahedron -d 1.3 -o box.gro genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro I typed: grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr where em.mdp is my energy minimization file and I got: Fatal error: Unknown bond_atomtype C2 What is here the problem? All atom types should be declared by me, I guess. Thanks for helping me Greetings Lara -- 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] grompp Unkown bond_atomtype C2
On 5/16/12 3:56 AM, Lara Bunte wrote: Hi After: pdb2gmx -f mymol.pdb -water tip3p editconf -f conf.gro -bt dodecahedron -d 1.3 -o box.gro genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro I typed: grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr where em.mdp is my energy minimization file and I got: Fatal error: Unknown bond_atomtype C2 What is here the problem? All atom types should be declared by me, I guess. You're making use of an atom type called C2 in some bonded interaction, but such an atom type doesn't exist. You need to define it. -Justin -- Justin A. Lemkul, Ph.D. 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] grompp Unkown bond_atomtype C2
Hi in my .rtp file I wrote in the [ atoms ] block C2 CN1A 0.7481 1 but in the atomtypes.atp file I wrote CN1A 12.01100 So I declared it. So what do you mean with such an atom type doesn't exist? Greetings Lara - Ursprüngliche Message - Von: Justin A. Lemkul jalem...@vt.edu An: Lara Bunte lara.bu...@yahoo.de; Discussion list for GROMACS users gmx-users@gromacs.org CC: Gesendet: 13:22 Mittwoch, 16.Mai 2012 Betreff: Re: [gmx-users] grompp Unkown bond_atomtype C2 On 5/16/12 3:56 AM, Lara Bunte wrote: Hi After: pdb2gmx -f mymol.pdb -water tip3p editconf -f conf.gro -bt dodecahedron -d 1.3 -o box.gro genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro I typed: grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr where em.mdp is my energy minimization file and I got: Fatal error: Unknown bond_atomtype C2 What is here the problem? All atom types should be declared by me, I guess. You're making use of an atom type called C2 in some bonded interaction, but such an atom type doesn't exist. You need to define it. -Justin -- Justin A. Lemkul, Ph.D. 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] grompp Unkown bond_atomtype C2
On 5/16/12 8:05 AM, Lara Bunte wrote: Hi in my .rtp file I wrote in the [ atoms ] block C2 CN1A0.7481 1 but in the atomtypes.atp file I wrote CN1A12.01100 So I declared it. So what do you mean with such an atom type doesn't exist? Neither of those actions constitutes what you need. Your atom name is C2, while its type is CN1A. Apparently somewhere in the bonded parameters you've assigned C2 as a type, which is wrong. You need to be using CN1A if adding a new bonded parameter. The CN1A atom type already exists in the force field so you don't need to do anything special. Note for the future that in order to add a new atom type (if necessary), it needs to have its parameters listed in ffbonded.itp. Mentioning it in the .rtp and .atp files does not do much for you; it simply makes that atom type accessible in the topology, but if it doesn't have parameters assigned, it is useless. -Justin -- Justin A. Lemkul, Ph.D. 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
[gmx-users] grompp error
Hello, I am doing solvation dynamics for my system. When I am running grompp command I get the error. grompp -f md.mdp -c solvent-bmi-pf6-128.pdb -p solvent-bmi-pf6-128.top -o md-rerun.tpr Fatal error: No such combination rule 0 I using Gromacs VERSION 4.0.5. What this error means? Thanks NIlesh -- 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] grompp error
On 4/22/12 11:49 PM, Nilesh Dhumal wrote: Hello, I am doing solvation dynamics for my system. When I am running grompp command I get the error. grompp -f md.mdp -c solvent-bmi-pf6-128.pdb -p solvent-bmi-pf6-128.top -o md-rerun.tpr Fatal error: No such combination rule 0 I using Gromacs VERSION 4.0.5. What this error means? It means what it says - your force field (presumably a custom one) is using an invalid combination rule. See manual section 5.3.3 for valid options, then check the [defaults] directive for your force field and amend appropriately. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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
[gmx-users] grompp error
Hi all, After i ran grompp I've the following message: Fatal error: 3 atoms are non part of any of the T-coupling groups It is probably in refference to the 3 CL atoms i've introduced into the system to neutralize my protein charge. Here are the command lines for genion and grompp genion_d -s arath_stpr.tpr -o arath_ions.gro -nname CL -nn 3 -nq -1 -p arath.top grommp_d -f stpr.mdp -c arath_ions.gro -p arath.top -o arath_stpr.tpr Additional information: I'm running GROMACS 4.5.5 Regards. -- 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] grompp error
Eduardo Oliveira wrote: Hi all, After i ran grompp I've the following message: Fatal error: 3 atoms are non part of any of the T-coupling groups It is probably in refference to the 3 CL atoms i've introduced into the system to neutralize my protein charge. Here are the command lines for genion and grompp genion_d -s arath_stpr.tpr -o arath_ions.gro -nname CL -nn 3 -nq -1 -p arath.top grommp_d -f stpr.mdp -c arath_ions.gro -p arath.top -o arath_stpr.tpr Additional information: I'm running GROMACS 4.5.5 What are your tc-grps? Please provide your .mdp file. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] grompp error
Probably consult the tutorials to determine what T-coupling groups to use. Generally, Water_and_ions with a separate Protein as 2 T-coupling groups when dealing with a globular protein in water, but you will have to determine if that is appropriate for your particular system (i.e. if there are ligands, multi-molecule complexes, etc. involved it will probably be different). On 2012-04-03 11:51:01AM -0700, Eduardo Oliveira wrote: Hi all, After i ran grompp I've the following message: Fatal error: 3 atoms are non part of any of the T-coupling groups It is probably in refference to the 3 CL atoms i've introduced into the system to neutralize my protein charge. Here are the command lines for genion and grompp genion_d -s arath_stpr.tpr -o arath_ions.gro -nname CL -nn 3 -nq -1 -p arath.top grommp_d -f stpr.mdp -c arath_ions.gro -p arath.top -o arath_stpr.tpr Additional information: I'm running GROMACS 4.5.5 Regards. -- 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 -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- 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] grompp error
Eduardo Oliveira wrote: Thanks! Please keep the discussion on the list. From your .mdp file: tc-grps = Protein SOL As I suspected, you're not accounting for ions in any way. You need to. Usually Protein Non-protein works just fine for simple systems. -Justin *De:* Justin A. Lemkul jalem...@vt.edu *Para:* Eduardo Oliveira eduardo...@yahoo.com.br; Discussion list for GROMACS users gmx-users@gromacs.org *Enviadas:* Terça-feira, 3 de Abril de 2012 15:54 *Assunto:* Re: [gmx-users] grompp error Eduardo Oliveira wrote: Hi all, After i ran grompp I've the following message: Fatal error: 3 atoms are non part of any of the T-coupling groups It is probably in refference to the 3 CL atoms i've introduced into the system to neutralize my protein charge. Here are the command lines for genion and grompp genion_d -s arath_stpr.tpr -o arath_ions.gro -nname CL -nn 3 -nq -1 -p arath.top grommp_d -f stpr.mdp -c arath_ions.gro -p arath.top -o arath_stpr.tpr Additional information: I'm running GROMACS 4.5.5 What are your tc-grps? Please provide your .mdp file. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] grompp error
Ok, thanks for the advice and sorry for sending the attached file. De: Justin A. Lemkul jalem...@vt.edu Para: Discussion list for GROMACS users gmx-users@gromacs.org Enviadas: Terça-feira, 3 de Abril de 2012 16:51 Assunto: Re: [gmx-users] grompp error Eduardo Oliveira wrote: Thanks! Please keep the discussion on the list. From your .mdp file: tc-grps = Protein SOL As I suspected, you're not accounting for ions in any way. You need to. Usually Protein Non-protein works just fine for simple systems. -Justin *De:* Justin A. Lemkul jalem...@vt.edu *Para:* Eduardo Oliveira eduardo...@yahoo.com.br; Discussion list for GROMACS users gmx-users@gromacs.org *Enviadas:* Terça-feira, 3 de Abril de 2012 15:54 *Assunto:* Re: [gmx-users] grompp error Eduardo Oliveira wrote: Hi all, After i ran grompp I've the following message: Fatal error: 3 atoms are non part of any of the T-coupling groups It is probably in refference to the 3 CL atoms i've introduced into the system to neutralize my protein charge. Here are the command lines for genion and grompp genion_d -s arath_stpr.tpr -o arath_ions.gro -nname CL -nn 3 -nq -1 -p arath.top grommp_d -f stpr.mdp -c arath_ions.gro -p arath.top -o arath_stpr.tpr Additional information: I'm running GROMACS 4.5.5 What are your tc-grps? Please provide your .mdp file. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 list gmx-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 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] grompp error
Eduardo Oliveira wrote: Ok, thanks for the advice and sorry for sending the attached file. No apology necessary; I asked for the file. I just ask that all discussion remain on the list, so that others can contribute and learn from it. -Justin *De:* Justin A. Lemkul jalem...@vt.edu *Para:* Discussion list for GROMACS users gmx-users@gromacs.org *Enviadas:* Terça-feira, 3 de Abril de 2012 16:51 *Assunto:* Re: [gmx-users] grompp error Eduardo Oliveira wrote: Thanks! Please keep the discussion on the list. From your .mdp file: tc-grps = Protein SOL As I suspected, you're not accounting for ions in any way. You need to. Usually Protein Non-protein works just fine for simple systems. -Justin *De:* Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu *Para:* Eduardo Oliveira eduardo...@yahoo.com.br mailto:eduardo...@yahoo.com.br; Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org *Enviadas:* Terça-feira, 3 de Abril de 2012 15:54 *Assunto:* Re: [gmx-users] grompp error Eduardo Oliveira wrote: Hi all, After i ran grompp I've the following message: Fatal error: 3 atoms are non part of any of the T-coupling groups It is probably in refference to the 3 CL atoms i've introduced into the system to neutralize my protein charge. Here are the command lines for genion and grompp genion_d -s arath_stpr.tpr -o arath_ions.gro -nname CL -nn 3 -nq -1 -p arath.top grommp_d -f stpr.mdp -c arath_ions.gro -p arath.top -o arath_stpr.tpr Additional information: I'm running GROMACS 4.5.5 What are your tc-grps? Please provide your .mdp file. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] grompp error
Ok, thanks again. That actually worked. De: Justin A. Lemkul jalem...@vt.edu Para: Discussion list for GROMACS users gmx-users@gromacs.org Enviadas: Terça-feira, 3 de Abril de 2012 18:30 Assunto: Re: [gmx-users] grompp error Eduardo Oliveira wrote: Ok, thanks for the advice and sorry for sending the attached file. No apology necessary; I asked for the file. I just ask that all discussion remain on the list, so that others can contribute and learn from it. -Justin *De:* Justin A. Lemkul jalem...@vt.edu *Para:* Discussion list for GROMACS users gmx-users@gromacs.org *Enviadas:* Terça-feira, 3 de Abril de 2012 16:51 *Assunto:* Re: [gmx-users] grompp error Eduardo Oliveira wrote: Thanks! Please keep the discussion on the list. From your .mdp file: tc-grps = Protein SOL As I suspected, you're not accounting for ions in any way. You need to. Usually Protein Non-protein works just fine for simple systems. -Justin *De:* Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu *Para:* Eduardo Oliveira eduardo...@yahoo.com.br mailto:eduardo...@yahoo.com.br; Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org *Enviadas:* Terça-feira, 3 de Abril de 2012 15:54 *Assunto:* Re: [gmx-users] grompp error Eduardo Oliveira wrote: Hi all, After i ran grompp I've the following message: Fatal error: 3 atoms are non part of any of the T-coupling groups It is probably in refference to the 3 CL atoms i've introduced into the system to neutralize my protein charge. Here are the command lines for genion and grompp genion_d -s arath_stpr.tpr -o arath_ions.gro -nname CL -nn 3 -nq -1 -p arath.top grommp_d -f stpr.mdp -c arath_ions.gro -p arath.top -o arath_stpr.tpr Additional information: I'm running GROMACS 4.5.5 What are your tc-grps? Please provide your .mdp file. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 list gmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 list gmx-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 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] grompp is adding a bond in my model that should not be there
On 26/03/2012 4:13 PM, Jackson Chief wrote: The missing residues correspond to a loop that connects two alpha helices. The C-terminal end of one helix, and N-terminal end of the other helix contain a random coil. After energy minimization, the coils are extended in space and not connected. I visualized this by looking at the .gro file in VMD. After 5ns of unrestrained MD, the two coils are clearly connected by looking at the output .gro file in VMD. Weird. The bonds you see are guessed by VMD from the coordinates. They have only fortuitous correlation with your system topology as constructed by pdb2gmx... which brings us back to you describing how you are treating the gap. The MD is apparently bringing the two termini close together, which is likely in response to a bonded interaction between them that you set up with your usage of pdb2gmx. If so, then it will have issued a warning about it... Mark On Sun, Mar 25, 2012 at 9:48 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 26/03/2012 12:20 PM, Jackson Chief wrote: I made a model of a receptor protein, bilayer, and solvent. My protein contains a 20 residue gap. This gap corresponds to a region of the protein that had been digested by trypsin before crystallization. The trypsin digestion has no affect on receptor activity experimentally. I performed energy minimization without problem. The protein looked like it should, containing the gap. You have to treat this gap somehow. Either you have to cap the peptide chains (see pdb2gmx -h), or model in the missing residues using some (non-GROMACS) software. When I performed equilibration, the output had the C-terminus of one protein fragment connected to the N-terminus of the other protein fragment. I don't know how this peptide bond was created, because it was not in the input *.gro file to grompp. Please help. .gro files have coordinates, never bonds. Since you haven't described how you are treating the gap, and haven't said how you've observed the creation of a peptide bond, it's hard to give specific guidance. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] grompp is adding a bond in my model that should not be there
I made a model of a receptor protein, bilayer, and solvent. My protein contains a 20 residue gap. This gap corresponds to a region of the protein that had been digested by trypsin before crystallization. The trypsin digestion has no affect on receptor activity experimentally. I performed energy minimization without problem. The protein looked like it should, containing the gap. When I performed equilibration, the output had the C-terminus of one protein fragment connected to the N-terminus of the other protein fragment. I don't know how this peptide bond was created, because it was not in the input *.gro file to grompp. Please help. Jackson Chief Elk Graduate Student in Biophysics and Biochemistry The University of Montana Missoula, MT -- 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] grompp is adding a bond in my model that should not be there
On 26/03/2012 12:20 PM, Jackson Chief wrote: I made a model of a receptor protein, bilayer, and solvent. My protein contains a 20 residue gap. This gap corresponds to a region of the protein that had been digested by trypsin before crystallization. The trypsin digestion has no affect on receptor activity experimentally. I performed energy minimization without problem. The protein looked like it should, containing the gap. You have to treat this gap somehow. Either you have to cap the peptide chains (see pdb2gmx -h), or model in the missing residues using some (non-GROMACS) software. When I performed equilibration, the output had the C-terminus of one protein fragment connected to the N-terminus of the other protein fragment. I don't know how this peptide bond was created, because it was not in the input *.gro file to grompp. Please help. .gro files have coordinates, never bonds. Since you haven't described how you are treating the gap, and haven't said how you've observed the creation of a peptide bond, it's hard to give specific guidance. Mark -- 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] grompp is adding a bond in my model that should not be there
The missing residues correspond to a loop that connects two alpha helices. The C-terminal end of one helix, and N-terminal end of the other helix contain a random coil. After energy minimization, the coils are extended in space and not connected. I visualized this by looking at the .gro file in VMD. After 5ns of unrestrained MD, the two coils are clearly connected by looking at the output .gro file in VMD. Weird. On Sun, Mar 25, 2012 at 9:48 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 26/03/2012 12:20 PM, Jackson Chief wrote: I made a model of a receptor protein, bilayer, and solvent. My protein contains a 20 residue gap. This gap corresponds to a region of the protein that had been digested by trypsin before crystallization. The trypsin digestion has no affect on receptor activity experimentally. I performed energy minimization without problem. The protein looked like it should, containing the gap. You have to treat this gap somehow. Either you have to cap the peptide chains (see pdb2gmx -h), or model in the missing residues using some (non-GROMACS) software. When I performed equilibration, the output had the C-terminus of one protein fragment connected to the N-terminus of the other protein fragment. I don't know how this peptide bond was created, because it was not in the input *.gro file to grompp. Please help. .gro files have coordinates, never bonds. Since you haven't described how you are treating the gap, and haven't said how you've observed the creation of a peptide bond, it's hard to give specific guidance. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] grompp is adding a bond in my model that should not be there
Hey, The problem is likely that pdb2gmx created the bond. It will have given a long bond warning. You can add a ter statement in the pdb file at the break. Cheers, Tsjerk On Mar 26, 2012 5:49 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 26/03/2012 12:20 PM, Jackson Chief wrote: I made a model of a receptor protein, bilayer, and ... You have to treat this gap somehow. Either you have to cap the peptide chains (see pdb2gmx -h), or model in the missing residues using some (non-GROMACS) software. When I performed equilibration, the output had the C-terminus of one protein fragment connecte... .gro files have coordinates, never bonds. Since you haven't described how you are treating the gap, and haven't said how you've observed the creation of a peptide bond, it's hard to give specific guidance. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] grompp - Group protein not found
Hi I want to solve my problem by creating an index file but I did not understand what I have to write in this file. I read the content in this link: http://manual.gromacs.org/online/ndx.html but I can't apply this to my problem. Could you please help? Thanks Greetings Lara - Ursprüngliche Message - Von: Mark Abraham mark.abra...@anu.edu.au An: Discussion list for GROMACS users gmx-users@gromacs.org CC: Gesendet: 21:41 Mittwoch, 7.März 2012 Betreff: Re: [gmx-users] grompp - Group protein not found On 8/03/2012 4:31 AM, Peter C. Lai wrote: Check the molecules section at the bottom of your top file. Each molecule entry there should match the corresponding name given to it in the molecule's own topology (the name under [moleculetype]). Those names can match and this error arise because this error is probably because the .mdp file refers to protein and there is no such group generated for the default index groups (used when no -n file is supplied). Either * make an index file with such a group and name it protein, * copy $GMXLIB/residuetypes.dat to your working directory and add your protein residues to allow the default generated groups to understand your knowledge about what is a protein, * name your [moleculetype] the same as your references to it in your .mdp file and [molecules] section. Mark On 2012-03-07 05:13:11PM +, Lara Bunte wrote: Hi I create a file pr.mdp for equilibrating the water around my molecule and used after that the command grompp -f pr.mdp -p topol.top -c em.gro -o pr.tpr And I got tthe error: Fatal error: Group protein not found in index file. Group names must match either [moleculetype] names or custom index group names,in which case you must supply an index file to the '-n' option of grompp. Could you explain that error to me please? How to fix it? Greetings Lara -- gmx-users mailing list gmx-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 mailing list gmx-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 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] grompp - Group protein not found
Hi, You need make_ndx: http://manual.gromacs.org/online/make_ndx.html This command gives you an interactive dialogue, in which you can select the atoms/residues/molecules you want to include in the index file. The selection is a bit tricky, but using the help function and looking at examples should get you there in the end. Best wishes Andreas From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Lara Bunte [lara.bu...@yahoo.de] Sent: 19 March 2012 16:11 To: Discussion list for GROMACS users Subject: Re: [gmx-users] grompp - Group protein not found Hi I want to solve my problem by creating an index file but I did not understand what I have to write in this file. I read the content in this link: http://manual.gromacs.org/online/ndx.html but I can't apply this to my problem. Could you please help? Thanks Greetings Lara - Ursprüngliche Message - Von: Mark Abraham mark.abra...@anu.edu.au An: Discussion list for GROMACS users gmx-users@gromacs.org CC: Gesendet: 21:41 Mittwoch, 7.März 2012 Betreff: Re: [gmx-users] grompp - Group protein not found On 8/03/2012 4:31 AM, Peter C. Lai wrote: Check the molecules section at the bottom of your top file. Each molecule entry there should match the corresponding name given to it in the molecule's own topology (the name under [moleculetype]). Those names can match and this error arise because this error is probably because the .mdp file refers to protein and there is no such group generated for the default index groups (used when no -n file is supplied). Either * make an index file with such a group and name it protein, * copy $GMXLIB/residuetypes.dat to your working directory and add your protein residues to allow the default generated groups to understand your knowledge about what is a protein, * name your [moleculetype] the same as your references to it in your .mdp file and [molecules] section. Mark On 2012-03-07 05:13:11PM +, Lara Bunte wrote: Hi I create a file pr.mdp for equilibrating the water around my molecule and used after that the command grompp -f pr.mdp -p topol.top -c em.gro -o pr.tpr And I got tthe error: Fatal error: Group protein not found in index file. Group names must match either [moleculetype] names or custom index group names,in which case you must supply an index file to the '-n' option of grompp. Could you explain that error to me please? How to fix it? Greetings Lara -- 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 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 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 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] grompp warning with SHAKE, but ok with LINCS
I trying to do an NVT simulation of a peptide in water with the following mdp parameters: title = GROMOS53A6 NVT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstxtcout = 100 ; save coordinates to trajectory every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation= no; first dynamics run ;bond constraint constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained constraint_algorithm = SHAKE; shake_tol = 0.0001; relative tolerance ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 0.8 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.4 ; short-range electrostatic cutoff (in nm) rvdw= 1.4 ; short-range van der Waals cutoff (in nm) ; Electrostatics and ven der Waals coulombtype = Reaction-Field ; reaction-field for long-range electrostatics vdw-type= Cut-off; van der Waals treatment for long-range electrostatics epsilon_rf = 62; dielectric constant/relative permitivitty ; Temperature coupling is on tcoupl = V-rescale; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t= 0.1 0.1 ; time constant, in ps ref_t= 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 300 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed == When I run grompp with the command: grompp -v -f pr.mdp -c protein_mod1_EM_solv.gro -p protein_mod1.top -o protein_mod1_PR.tpr I get a warning which reads: WARNING 1 [file 1DU9_mod1.top, line 1651]: With twin-range cut-off's and SHAKE the virial and the pressure are incorrect. However, when I delete the constraint_algorithm and shake_tol prameters from the mdp file allowing grompp to use the defualt LINCS algorithm, grompp doesn't complaint. Can any one help me as to why grompp complains when SHAKE is used but not with LINCS? The forcefield paper used SHAKE as constraint algorithm. Should I stay with SHAKE or use LINCS instead? By the way I am using GROMOS53A6 force field for the simulation. Thanks all. - Research Assistant Sikkim Manipal University DE -- View this message in context: http://gromacs.5086.n6.nabble.com/grompp-warning-with-SHAKE-but-ok-with-LINCS-tp4627513p4627513.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] grompp warning with SHAKE, but ok with LINCS
Hi D_Roy, The warning message is quite self-explanatory. Do read beyond the word WARNING. As for the other question, the constraint algorithm stands apart from the forcefield, unlike many other options. You can safely use Lincs with G536. Cheers, Tsjerk On Mar 17, 2012 10:31 AM, D_Roy r.dipan...@gmail.com wrote: I trying to do an NVT simulation of a peptide in water with the following mdp parameters: title = GROMOS53A6 NVT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstxtcout = 100 ; save coordinates to trajectory every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation= no; first dynamics run ;bond constraint constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained constraint_algorithm = SHAKE; shake_tol = 0.0001; relative tolerance ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 0.8 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.4 ; short-range electrostatic cutoff (in nm) rvdw= 1.4 ; short-range van der Waals cutoff (in nm) ; Electrostatics and ven der Waals coulombtype = Reaction-Field ; reaction-field for long-range electrostatics vdw-type= Cut-off; van der Waals treatment for long-range electrostatics epsilon_rf = 62; dielectric constant/relative permitivitty ; Temperature coupling is on tcoupl = V-rescale; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t= 0.1 0.1 ; time constant, in ps ref_t= 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 300 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed == When I run grompp with the command: grompp -v -f pr.mdp -c protein_mod1_EM_solv.gro -p protein_mod1.top -o protein_mod1_PR.tpr I get a warning which reads: WARNING 1 [file 1DU9_mod1.top, line 1651]: With twin-range cut-off's and SHAKE the virial and the pressure are incorrect. However, when I delete the constraint_algorithm and shake_tol prameters from the mdp file allowing grompp to use the defualt LINCS algorithm, grompp doesn't complaint. Can any one help me as to why grompp complains when SHAKE is used but not with LINCS? The forcefield paper used SHAKE as constraint algorithm. Should I stay with SHAKE or use LINCS instead? By the way I am using GROMOS53A6 force field for the simulation. Thanks all. - Research Assistant Sikkim Manipal University DE -- View this message in context: http://gromacs.5086.n6.nabble.com/grompp-warning-with-SHAKE-but-ok-with-LINCS-tp4627513p4627513.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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 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] grompp - Group protein not found
Hi Mark Could you please explain your hints in more detail. I do not understand what you are saying. What do you mean with: error is probably because the .mdp file refers to protein and there is no such group generated for the default index groups (used when no -n file is supplied) And could you explain this? * make an index file with such a group and name it protein, * copy $GMXLIB/residuetypes.dat to your working directory and add your protein residues to allow the default generated groups to understand your knowledge about what is a protein, * name your [moleculetype] the same as your references to it in your .mdp file and [molecules] section. Thanks you Greetings Lara - Ursprüngliche Message - Von: Mark Abraham mark.abra...@anu.edu.au An: Discussion list for GROMACS users gmx-users@gromacs.org CC: Gesendet: 21:41 Mittwoch, 7.März 2012 Betreff: Re: [gmx-users] grompp - Group protein not found On 8/03/2012 4:31 AM, Peter C. Lai wrote: Check the molecules section at the bottom of your top file. Each molecule entry there should match the corresponding name given to it in the molecule's own topology (the name under [moleculetype]). Those names can match and this error arise because this error is probably because the .mdp file refers to protein and there is no such group generated for the default index groups (used when no -n file is supplied). Either * make an index file with such a group and name it protein, * copy $GMXLIB/residuetypes.dat to your working directory and add your protein residues to allow the default generated groups to understand your knowledge about what is a protein, * name your [moleculetype] the same as your references to it in your .mdp file and [molecules] section. Mark On 2012-03-07 05:13:11PM +, Lara Bunte wrote: Hi I create a file pr.mdp for equilibrating the water around my molecule and used after that the command grompp -f pr.mdp -p topol.top -c em.gro -o pr.tpr And I got tthe error: Fatal error: Group protein not found in index file. Group names must match either [moleculetype] names or custom index group names,in which case you must supply an index file to the '-n' option of grompp. Could you explain that error to me please? How to fix it? Greetings Lara -- gmx-users mailing list gmx-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 mailing list gmx-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 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] grompp - Group protein not found
On 9/03/2012 11:15 PM, Lara Bunte wrote: Hi Mark Could you please explain your hints in more detail. I do not understand what you are saying. What do you mean with: error is probably because the .mdp file refers to protein and there is no such group generated for the default index groups (used when no -n file is supplied) And could you explain this? No. You're making it hard to help you by supplying no information about your simulation system, GROMACS version or .mdp file. See http://www.gromacs.org/Support. Mark * make an index file with such a group and name it protein, * copy $GMXLIB/residuetypes.dat to your working directory and add your protein residues to allow the default generated groups to understand your knowledge about what is a protein, * name your [moleculetype] the same as your references to it in your .mdp file and [molecules] section. Thanks you Greetings Lara - Ursprüngliche Message - Von: Mark Abrahammark.abra...@anu.edu.au An: Discussion list for GROMACS usersgmx-users@gromacs.org CC: Gesendet: 21:41 Mittwoch, 7.März 2012 Betreff: Re: [gmx-users] grompp - Group protein not found On 8/03/2012 4:31 AM, Peter C. Lai wrote: Check the molecules section at the bottom of your top file. Each molecule entry there should match the corresponding name given to it in the molecule's own topology (the name under [moleculetype]). Those names can match and this error arise because this error is probably because the .mdp file refers to protein and there is no such group generated for the default index groups (used when no -n file is supplied). Either * make an index file with such a group and name it protein, * copy $GMXLIB/residuetypes.dat to your working directory and add your protein residues to allow the default generated groups to understand your knowledge about what is a protein, * name your [moleculetype] the same as your references to it in your .mdp file and [molecules] section. Mark On 2012-03-07 05:13:11PM +, Lara Bunte wrote: Hi I create a file pr.mdp for equilibrating the water around my molecule and used after that the command grompp -f pr.mdp -p topol.top -c em.gro -o pr.tpr And I got tthe error: Fatal error: Group protein not found in index file. Group names must match either [moleculetype] names or custom index group names,in which case you must supply an index file to the '-n' option of grompp. Could you explain that error to me please? How to fix it? Greetings Lara -- 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 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 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] grompp - Group protein not found
Hi I create a file pr.mdp for equilibrating the water around my molecule and used after that the command grompp -f pr.mdp -p topol.top -c em.gro -o pr.tpr And I got tthe error: Fatal error: Group protein not found in index file. Group names must match either [moleculetype] names or custom index group names,in which case you must supply an index file to the '-n' option of grompp. Could you explain that error to me please? How to fix it? Greetings Lara -- 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] grompp - Group protein not found
Check the molecules section at the bottom of your top file. Each molecule entry there should match the corresponding name given to it in the molecule's own topology (the name under [moleculetype]). On 2012-03-07 05:13:11PM +, Lara Bunte wrote: Hi I create a file pr.mdp for equilibrating the water around my molecule and used after that the command grompp -f pr.mdp -p topol.top -c em.gro -o pr.tpr And I got tthe error: Fatal error: Group protein not found in index file. Group names must match either [moleculetype] names or custom index group names,in which case you must supply an index file to the '-n' option of grompp. Could you explain that error to me please? How to fix it? Greetings Lara -- 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 -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- 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] grompp - Group protein not found
On 8/03/2012 4:31 AM, Peter C. Lai wrote: Check the molecules section at the bottom of your top file. Each molecule entry there should match the corresponding name given to it in the molecule's own topology (the name under [moleculetype]). Those names can match and this error arise because this error is probably because the .mdp file refers to protein and there is no such group generated for the default index groups (used when no -n file is supplied). Either * make an index file with such a group and name it protein, * copy $GMXLIB/residuetypes.dat to your working directory and add your protein residues to allow the default generated groups to understand your knowledge about what is a protein, * name your [moleculetype] the same as your references to it in your .mdp file and [molecules] section. Mark On 2012-03-07 05:13:11PM +, Lara Bunte wrote: Hi I create a file pr.mdp for equilibrating the water around my molecule and used after that the command grompp -f pr.mdp -p topol.top -c em.gro -o pr.tpr And I got tthe error: Fatal error: Group protein not found in index file. Group names must match either [moleculetype] names or custom index group names,in which case you must supply an index file to the '-n' option of grompp. Could you explain that error to me please? How to fix it? Greetings Lara -- 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 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] grompp - Group protein not found
Ahh, case sensitivity? Protein vs. protein? On 2012-03-08 07:41:15AM +1100, Mark Abraham wrote: On 8/03/2012 4:31 AM, Peter C. Lai wrote: Check the molecules section at the bottom of your top file. Each molecule entry there should match the corresponding name given to it in the molecule's own topology (the name under [moleculetype]). Those names can match and this error arise because this error is probably because the .mdp file refers to protein and there is no such group generated for the default index groups (used when no -n file is supplied). Either * make an index file with such a group and name it protein, * copy $GMXLIB/residuetypes.dat to your working directory and add your protein residues to allow the default generated groups to understand your knowledge about what is a protein, * name your [moleculetype] the same as your references to it in your .mdp file and [molecules] section. Mark On 2012-03-07 05:13:11PM +, Lara Bunte wrote: Hi I create a file pr.mdp for equilibrating the water around my molecule and used after that the command grompp -f pr.mdp -p topol.top -c em.gro -o pr.tpr And I got tthe error: Fatal error: Group protein not found in index file. Group names must match either [moleculetype] names or custom index group names,in which case you must supply an index file to the '-n' option of grompp. Could you explain that error to me please? How to fix it? Greetings Lara -- 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 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 -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- 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] grompp - Group protein not found
On 8/03/2012 7:59 AM, Peter C. Lai wrote: Ahh, case sensitivity? Protein vs. protein? No. Mark On 2012-03-08 07:41:15AM +1100, Mark Abraham wrote: On 8/03/2012 4:31 AM, Peter C. Lai wrote: Check the molecules section at the bottom of your top file. Each molecule entry there should match the corresponding name given to it in the molecule's own topology (the name under [moleculetype]). Those names can match and this error arise because this error is probably because the .mdp file refers to protein and there is no such group generated for the default index groups (used when no -n file is supplied). Either * make an index file with such a group and name it protein, * copy $GMXLIB/residuetypes.dat to your working directory and add your protein residues to allow the default generated groups to understand your knowledge about what is a protein, * name your [moleculetype] the same as your references to it in your .mdp file and [molecules] section. Mark On 2012-03-07 05:13:11PM +, Lara Bunte wrote: Hi I create a file pr.mdp for equilibrating the water around my molecule and used after that the command grompp -f pr.mdp -p topol.top -c em.gro -o pr.tpr And I got tthe error: Fatal error: Group protein not found in index file. Group names must match either [moleculetype] names or custom index group names,in which case you must supply an index file to the '-n' option of grompp. Could you explain that error to me please? How to fix it? Greetings Lara -- 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 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 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] grompp - Invalid command line argument
Hi I used the command grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr and got the error Source code file: /home/adrian/src/gromacs-4.5.5/src/gmxlib/statutil.c, line: 819 Invalid command line argument: em.tpr What is the problem here? Greetings Lara -- 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] grompp - Invalid command line argument
Lara Bunte wrote: Hi I used the command grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr and got the error Source code file: /home/adrian/src/gromacs-4.5.5/src/gmxlib/statutil.c, line: 819 Invalid command line argument: em.tpr What is the problem here? The command posted above is syntactically correct, so it's not what you typed ;) Check carefully for typos and spacing, particularly if you have mis-spaced or omitted the -o flag, which would cause the file name to be incorrectly interpreted. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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
[gmx-users] grompp error - bondedtypes
Hi I used the command grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr and get this errors: ERROR 1 [file flavin.rtp, line 1]: Invalid directive bondedtypes ERROR 2 [file flavin.rtp, line 7]: Not enough parameters I know where this error occurs from but I don't know what is false. Could you please take a look on my files, see appendix. Thanks Greetings Lara topol.top Description: Binary data flavin.rtp Description: Binary data -- 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] grompp error - bondedtypes
Lara Bunte wrote: Hi I used the command grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr and get this errors: ERROR 1 [file flavin.rtp, line 1]: Invalid directive bondedtypes ERROR 2 [file flavin.rtp, line 7]: Not enough parameters I know where this error occurs from but I don't know what is false. Could you please take a look on my files, see appendix. grompp should never read .rtp files, so somewhere in your files you're likely trying to #include it or otherwise invoke it. There is no indication of this in your topology, so we can't tell where the error is. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] grompp error - bondedtypes
Lara Bunte wrote: Yes it was included in forcefield.itp Only pdb2gmx uses .rtp files (see the manual). Thanks for your help Know I got the error No default Fourier Dih. types What should I do? You need a corresponding [dihedraltypes] for all dihedrals in the system. The error indicates there is a dihedral for which parameters do not exist. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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:Re: [gmx-users] grompp error - bondedtypes
Justin A. Lemkul jalem...@vt.edu wrote: Lara Bunte wrote: Yes it was included in forcefield.itp Only pdb2gmx uses .rtp files (see the manual). Thanks for your help Know I got the error No default Fourier Dih. types What should I do? You need a corresponding [dihedraltypes] for all dihedrals in the system. The error indicates there is a dihedral for which parameters do not exist. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 -- 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] grompp g96angle types error
Dear all, I launch those commands for few models : pdb2gmx -f 2it7-10_bestene1mc-SC.pdb -o 2it7-10_bestene1mc-SC.gro -p 2it7-10_bestene1mc-SC.top -ignh -missing editconf -f 2it7-10_bestene1mc-SC.gro -o 2it7-10_bestene1mc-SC-box.gro -d 2.0 -c -bt cubic grompp -c 2it7-10_bestene1mc-SC-box.gro -p 2it7-10_bestene1mc-SC.top -o 2it7-10_bestene1mc-SC-min.tpr -f 2it7-10_bestene1mc-SC-em.mdp and at the grompp command I obtain : checking input for internal consistency... calling /lib/cpp... processing topology... Generated 165 of the 1596 non-bonded parameter combinations ERROR 0 [file 2it7-10_bestene1mc-SC.top, line 1242]: No default G96Angle types Excluding 3 bonded neighbours for Protein 1 NOTE: System has non-zero total charge: 1.00e+00 processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... # G96BONDS: 254 # G96ANGLES: 367 # PDIHS: 149 # IDIHS: 108 # LJ14: 436 I don't understand the meaning of: No default G96Angle types. All my files are generated by the same way, with the same softwares, and the sames options. All the models are done by the same software so the .pdb file only the coordinates of the protein change for one model to another. Can you help me? Thanks, Pierre THEVENET -- 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] grompp g96angle types error
pitheve...@free.fr wrote: Dear all, I launch those commands for few models : pdb2gmx -f 2it7-10_bestene1mc-SC.pdb -o 2it7-10_bestene1mc-SC.gro -p 2it7-10_bestene1mc-SC.top -ignh -missing editconf -f 2it7-10_bestene1mc-SC.gro -o 2it7-10_bestene1mc-SC-box.gro -d 2.0 -c -bt cubic grompp -c 2it7-10_bestene1mc-SC-box.gro -p 2it7-10_bestene1mc-SC.top -o 2it7-10_bestene1mc-SC-min.tpr -f 2it7-10_bestene1mc-SC-em.mdp and at the grompp command I obtain : checking input for internal consistency... calling /lib/cpp... processing topology... Generated 165 of the 1596 non-bonded parameter combinations ERROR 0 [file 2it7-10_bestene1mc-SC.top, line 1242]: No default G96Angle types Excluding 3 bonded neighbours for Protein 1 NOTE: System has non-zero total charge: 1.00e+00 processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... # G96BONDS: 254 # G96ANGLES: 367 # PDIHS: 149 # IDIHS: 108 # LJ14: 436 I don't understand the meaning of: No default G96Angle types. All my files are generated by the same way, with the same softwares, and the sames options. All the models are done by the same software so the .pdb file only the coordinates of the protein change for one model to another. Can you help me? The error message indicates that angle parameters do not exist in the chosen force field for a certain sequence of atoms. This would be highly unusual for a standard protein. Are you using any custom residues? The error message indicates the line in the .top that is causing the problem. Look it up, find which atoms it corresponds to, and check ffbonded.itp to verify that suitable parameters are indeed not present. If you're using some kind of custom residue or nonstandard composition of atoms, then you'll likely have to parameterize the missing term(s) yourself. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] grompp g96angle types error
pitheve...@free.fr wrote: The problem seems to be between 3 S of CYS residues. I only use the 20 usual residues and with no modifications. An angle involving three S atoms? That should never occur. Where is the ffbonded.itp file? It's in $GMXLIB, i.e. the /share/gromacs/top subdirectory of your Gromacs installation. If the problematic angle is indeed S-S-S, I guarantee you won't find it there, though. -Justin Thank you, Pierre THEVENET - Mail original - De: Justin A. Lemkul jalem...@vt.edu À: Discussion list for GROMACS users gmx-users@gromacs.org Envoyé: Mardi 17 Janvier 2012 15:12:58 Objet: Re: [gmx-users] grompp g96angle types error pitheve...@free.fr wrote: Dear all, I launch those commands for few models : pdb2gmx -f 2it7-10_bestene1mc-SC.pdb -o 2it7-10_bestene1mc-SC.gro -p 2it7-10_bestene1mc-SC.top -ignh -missing editconf -f 2it7-10_bestene1mc-SC.gro -o 2it7-10_bestene1mc-SC-box.gro -d 2.0 -c -bt cubic grompp -c 2it7-10_bestene1mc-SC-box.gro -p 2it7-10_bestene1mc-SC.top -o 2it7-10_bestene1mc-SC-min.tpr -f 2it7-10_bestene1mc-SC-em.mdp and at the grompp command I obtain : checking input for internal consistency... calling /lib/cpp... processing topology... Generated 165 of the 1596 non-bonded parameter combinations ERROR 0 [file 2it7-10_bestene1mc-SC.top, line 1242]: No default G96Angle types Excluding 3 bonded neighbours for Protein 1 NOTE: System has non-zero total charge: 1.00e+00 processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... # G96BONDS: 254 # G96ANGLES: 367 # PDIHS: 149 # IDIHS: 108 # LJ14: 436 I don't understand the meaning of: No default G96Angle types. All my files are generated by the same way, with the same softwares, and the sames options. All the models are done by the same software so the .pdb file only the coordinates of the protein change for one model to another. Can you help me? The error message indicates that angle parameters do not exist in the chosen force field for a certain sequence of atoms. This would be highly unusual for a standard protein. Are you using any custom residues? The error message indicates the line in the .top that is causing the problem. Look it up, find which atoms it corresponds to, and check ffbonded.itp to verify that suitable parameters are indeed not present. If you're using some kind of custom residue or nonstandard composition of atoms, then you'll likely have to parameterize the missing term(s) yourself. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] grompp g96angle types error
Ok! The problem doesn't really come from gromacs so. It's my side-chain positioning software which made this... I'll try to fix it. Thank you very much. Pierre THEVEVENET - Mail original - De: Justin A. Lemkul jalem...@vt.edu À: Discussion list for GROMACS users gmx-users@gromacs.org Envoyé: Mardi 17 Janvier 2012 15:30:08 Objet: Re: [gmx-users] grompp g96angle types error pitheve...@free.fr wrote: The problem seems to be between 3 S of CYS residues. I only use the 20 usual residues and with no modifications. An angle involving three S atoms? That should never occur. Where is the ffbonded.itp file? It's in $GMXLIB, i.e. the /share/gromacs/top subdirectory of your Gromacs installation. If the problematic angle is indeed S-S-S, I guarantee you won't find it there, though. -Justin Thank you, Pierre THEVENET - Mail original - De: Justin A. Lemkul jalem...@vt.edu À: Discussion list for GROMACS users gmx-users@gromacs.org Envoyé: Mardi 17 Janvier 2012 15:12:58 Objet: Re: [gmx-users] grompp g96angle types error pitheve...@free.fr wrote: Dear all, I launch those commands for few models : pdb2gmx -f 2it7-10_bestene1mc-SC.pdb -o 2it7-10_bestene1mc-SC.gro -p 2it7-10_bestene1mc-SC.top -ignh -missing editconf -f 2it7-10_bestene1mc-SC.gro -o 2it7-10_bestene1mc-SC-box.gro -d 2.0 -c -bt cubic grompp -c 2it7-10_bestene1mc-SC-box.gro -p 2it7-10_bestene1mc-SC.top -o 2it7-10_bestene1mc-SC-min.tpr -f 2it7-10_bestene1mc-SC-em.mdp and at the grompp command I obtain : checking input for internal consistency... calling /lib/cpp... processing topology... Generated 165 of the 1596 non-bonded parameter combinations ERROR 0 [file 2it7-10_bestene1mc-SC.top, line 1242]: No default G96Angle types Excluding 3 bonded neighbours for Protein 1 NOTE: System has non-zero total charge: 1.00e+00 processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... # G96BONDS: 254 # G96ANGLES: 367 # PDIHS: 149 # IDIHS: 108 # LJ14: 436 I don't understand the meaning of: No default G96Angle types. All my files are generated by the same way, with the same softwares, and the sames options. All the models are done by the same software so the .pdb file only the coordinates of the protein change for one model to another. Can you help me? The error message indicates that angle parameters do not exist in the chosen force field for a certain sequence of atoms. This would be highly unusual for a standard protein. Are you using any custom residues? The error message indicates the line in the .top that is causing the problem. Look it up, find which atoms it corresponds to, and check ffbonded.itp to verify that suitable parameters are indeed not present. If you're using some kind of custom residue or nonstandard composition of atoms, then you'll likely have to parameterize the missing term(s) yourself. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 -- 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] grompp error for CNT+surfactant simulation
Dear all I am using Gromacs 4.5.3 to simulate a system including: CNT+water+surfactant and I want to use opls force field for my whole system. so far I have done following things: 1.I copied oplsaa.ff folder in my working directory. 2.I added following lines to atomname2type.n2t Copls_9950 12.011 1C 0.142 Copls_9960 12.011 2C 0.142 C 0.142 Copls_9970 12.011 3C 0.142 C 0.142 C 0.142 Copls_9980 12.011 4C 0.142 C 0.142 C 0.142 C 0.142 3.I added these to ffbonded.itp [ bondtypes ] C C 1 0.14210 478900 [ angletypes ] C C C 1 120.000 397.480 [ dihedraltypes ] C C 1 0.000 167.360 1 4.I added these to ffnonbonded.itp opls_995 C 612.01100 0.000 A3.851000e-01 4.39600e-01 opls_996 C 612.01100 0.000 A3.851000e-01 4.39600e-01 opls_997 C 612.01100 0.000 A3.851000e-01 4.39600e-01 opls_998 C 612.01100 0.000 A3.851000e-01 4.39600e-01 5.I used g_x2top to create topology for CNT. Command line was: g_x2top -f cnt.pdb -o cnt.top -r cnt.rtp -name CNT -nexcl 5 6.I used TopolGen to produce the *.itp file for surfactant molecule. 7.I placed surfactant molecules around CNT. 8.I used editconf using this command: editconf -f cnt_sur.pdb -o cnt_sur.gro -c -d 1 -bt cubic 9. I wrote a a .top file given below, Include forcefield parameters #include ./oplsaa.ff/forcefield.itp ; Include topology for DTAB #include DTAB.itp ; Include topology for CNT #include cnt.itp ; [ molecules ] ; molecule name nr. DTAB 14 CNT 1 10.I called genbox with the command: genbox -cp cnt_sur.gro -cs spc216.gro -p topol.top -o solv.gro 11.I added manually these to topol.top ; Include SPC water topology #include oplsaa.ff/spc.itp 12. once I run grompp : grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr I got following errors: Ignoring obsolete mdp entry 'title' WARNING 1 [file ffbonded.itp, line 2704]: Overriding Bond parameters. old: 0.151 292880 0.151 292880 new: C C 1 0.14210 478900 Generated 335790 of the 335790 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 335790 of the 335790 1-4 parameter combinations ERROR 1 [file DTAB.itp, line 104]: No default Bond types ERROR 2 [file DTAB.itp, line 105]: No default Bond types ERROR 3 [file DTAB.itp, line 241]: No default Angle types ERROR 4 [file DTAB.itp, line 242]: No default Angle types ERROR 5 [file DTAB.itp, line 244]: No default Angle types ERROR 6 [file DTAB.itp, line 245]: No default Angle types ERROR 7 [file DTAB.itp, line 249]: No default Angle types ERROR 8 [file DTAB.itp, line 302]: No default Ryckaert-Bell. types ERROR 9 [file DTAB.itp, line 303]: No default Ryckaert-Bell. types Excluding 3 bonded neighbours molecule type 'DTAB' Excluding 5 bonded neighbours molecule type 'CNT' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file topol.top, line 27]: System has non-zero total charge: 5.03e+00 There was 1 note There was 1 warning --- Program grompp, VERSION 4.5.3 Source code file: /build/buildd/gromacs-4.5.3/src/kernel/grompp.c, line: 1356 Fatal error: There were 9 errors in input file(s) --- I would be more than pleased if someone could guild me how to solve the problem. -- 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] grompp error for CNT+surfactant simulation
niaz poorgholami wrote: Dear all I am using Gromacs 4.5.3 to simulate a system including: CNT+water+surfactant and I want to use opls force field for my whole system. so far I have done following things: 1.I copied oplsaa.ff folder in my working directory. 2.I added following lines to atomname2type.n2t Copls_9950 12.011 1C 0.142 Copls_9960 12.011 2C 0.142 C 0.142 Copls_9970 12.011 3C 0.142 C 0.142 C 0.142 Copls_9980 12.011 4C 0.142 C 0.142 C 0.142 C 0.142 3.I added these to ffbonded.itp [ bondtypes ] C C 1 0.14210 478900 [ angletypes ] C C C 1 120.000 397.480 [ dihedraltypes ] C C 1 0.000 167.360 1 4.I added these to ffnonbonded.itp opls_995 C 612.01100 0.000 A3.851000e-01 4.39600e-01 opls_996 C 612.01100 0.000 A3.851000e-01 4.39600e-01 opls_997 C 612.01100 0.000 A3.851000e-01 4.39600e-01 opls_998 C 612.01100 0.000 A3.851000e-01 4.39600e-01 5.I used g_x2top to create topology for CNT. Command line was: g_x2top -f cnt.pdb -o cnt.top -r cnt.rtp -name CNT -nexcl 5 6.I used TopolGen to produce the *.itp file for surfactant molecule. 7.I placed surfactant molecules around CNT. 8.I used editconf using this command: editconf -f cnt_sur.pdb -o cnt_sur.gro -c -d 1 -bt cubic 9. I wrote a a .top file given below, Include forcefield parameters #include ./oplsaa.ff/forcefield.itp ; Include topology for DTAB #include DTAB.itp ; Include topology for CNT #include cnt.itp ; [ molecules ] ; molecule name nr. DTAB 14 CNT 1 10.I called genbox with the command: genbox -cp cnt_sur.gro -cs spc216.gro -p topol.top -o solv.gro 11.I added manually these to topol.top ; Include SPC water topology #include oplsaa.ff/spc.itp 12. once I run grompp : grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr I got following errors: Ignoring obsolete mdp entry 'title' WARNING 1 [file ffbonded.itp, line 2704]: Overriding Bond parameters. old: 0.151 292880 0.151 292880 new: C C 1 0.14210 478900 So here grompp finds that you're overriding default force field parameters by using some customized bond types. This may or may not be what you want/need, so check carefully. If these are indeed what you are after, then there is no problem here. Generated 335790 of the 335790 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 335790 of the 335790 1-4 parameter combinations ERROR 1 [file DTAB.itp, line 104]: No default Bond types To solve this error and the subsequent ones, check your topology at the quoted line, identify which atom types the interaction pertains to, and determine which parameters need to be added to ffbonded.itp. The no default types error comes from the situation in which grompp cannot assign any parameters to the listed interaction. ERROR 2 [file DTAB.itp, line 105]: No default Bond types ERROR 3 [file DTAB.itp, line 241]: No default Angle types ERROR 4 [file DTAB.itp, line 242]: No default Angle types ERROR 5 [file DTAB.itp, line 244]: No default Angle types ERROR 6 [file DTAB.itp, line 245]: No default Angle types ERROR 7 [file DTAB.itp, line 249]: No default Angle types ERROR 8 [file DTAB.itp, line 302]: No default Ryckaert-Bell. types ERROR 9 [file DTAB.itp, line 303]: No default Ryckaert-Bell. types Excluding 3 bonded neighbours molecule type 'DTAB' Excluding 5 bonded neighbours molecule type 'CNT' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file topol.top, line 27]: System has non-zero total charge: 5.03e+00 The fractional net charge here indicates that at least one of the topologies (.itp) is broken such that you get a nonsensical sum of charges. It needs to be an integer. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] grompp error for CNT simulation
niaz poorgholami wrote: Dear gmx users, I am using gromacs 4.5.3 to simulate CNT in water. up to now I have done these things: 1. I used packmol to create my PDB file and the used editconf to change PDB to gro file. 2. I copied oplsaa.ff folder in my working directory 3. I added following lines to atomname2type.n2t Copls_9950 12.011 2C 0.142 C 0.142 Copls_9960 12.011 3C 0.142 C 0.142 C 0.142 Copls_9970 12.011 4C 0.142 C 0.142 C 0.142 C 0.142 Copls_9980 12.011 5C 0.142 C 0.142 C 0.142 C 0.142 C 0.142 4. I added these to atomtypes.atp opls_995 12.01100 opls_996 12.01100 opls_997 12.01100 opls_998 12.01100 5. I added these to ffbonded.itp [ bondtypes ] C C 1 0.14210 478900 [ angletypes ] C C C 1 120.000 397.480 [ dihedraltypes ] C C 1 0.000 167.360 1 6. I used g_x2top to create topology for CNT. Command line was: g_x2top -f CNT.gro -o CNT.top -pbc -nopairs -name CNT -nexcl 5 7. I wrote a .top file given below, ; Include forcefield parameters #include ./oplsaa.ff/forcefield.itp ; Include topology for water #include oplsaa.ff/spc.itp ; Include topology for CNT #include oplsaa.ff/CNT.itp [ system ] ; Name SDS and CNT in water [ molecules ] ; Compound#mols water 9000 CNT 1 8. when I run grompp for EM with this command line :grompp -f md.mdp -c cnt_alone.gro -p topol.top -o em.tpr it gave me the following error:Atomtype opls_995 not found. atomtypes.atp is only read by pdb2gmx. You need to introduce the proper nonbonded parameters for your new atom types in ffnonbonded.itp. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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
[gmx-users] grompp error for CNT simulation
Dear gmx users, I am using gromacs 4.5.3 to simulate CNT in water. up to now I have done these things: 1. I used packmol to create my PDB file and the used editconf to change PDB to gro file. 2. I copied oplsaa.ff folder in my working directory 3. I added following lines to atomname2type.n2t Copls_9950 12.011 2C 0.142 C 0.142 Copls_9960 12.011 3C 0.142 C 0.142 C 0.142 Copls_9970 12.011 4C 0.142 C 0.142 C 0.142 C 0.142 Copls_9980 12.011 5C 0.142 C 0.142 C 0.142 C 0.142 C 0.142 4. I added these to atomtypes.atp opls_995 12.01100 opls_996 12.01100 opls_997 12.01100 opls_998 12.01100 5. I added these to ffbonded.itp [ bondtypes ] C C 1 0.14210 478900 [ angletypes ] C C C 1 120.000 397.480 [ dihedraltypes ] C C 1 0.000 167.360 1 6. I used g_x2top to create topology for CNT. Command line was: g_x2top -f CNT.gro -o CNT.top -pbc -nopairs -name CNT -nexcl 5 7. I wrote a .top file given below, ; Include forcefield parameters #include ./oplsaa.ff/forcefield.itp ; Include topology for water #include oplsaa.ff/spc.itp ; Include topology for CNT #include oplsaa.ff/CNT.itp [ system ] ; Name SDS and CNT in water [ molecules ] ; Compound#mols water 9000 CNT 1 8. when I run grompp for EM with this command line :grompp -f md.mdp -c cnt_alone.gro -p topol.top -o em.tpr it gave me the following error:Atomtype opls_995 not found. I would be pleased if anyone could help me how to fix this. niaz -- 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] grompp error
Dear Sir' When I ran the grompp as following grompp -v -f md.mdp -c pr.gro -p RI-10.top -o md.tpr a error information appeared: Program grompp, VERSION 3.3.1 Source code file: readir.c, line: 789 Fatal error: Group Ptotein not found in indexfile Maybe you have non-default goups in your mdp file, while not using the '-n' opti on of grompp. In that case use the '-n' option I don't know which file Group Ptotein is in and where I should make change. Can you help me? Thanks in advance. Yeping Sun CAS Key Laboratory of Pathogenic Microbiology Immunology INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china-- 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] grompp error
On 25/11/2011 7:09 PM, yp sun wrote: Dear Sir' When I ran the grompp as following grompp -v -f md.mdp -c pr.gro -p RI-10.top -o md.tpr a error information appeared: Program grompp, VERSION 3.3.1 Source code file: readir.c, line: 789 Fatal error: Group Ptotein not found in indexfile Maybe you have non-default goups in your mdp file, while not using the '-n' opti on of grompp. In that case use the '-n' option I don't know which file Group Ptotein is in and where I should make change. Can you help me? Thanks in advance. You have referred to this group somewhere in your .mdp file, probably in error for Protein. grompp went looking in the index file (possibly generated by default) and was confused when it didn't find what you told it was there to be found. Mark -- 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] grompp error
The most reasonable thing is that there is a typo in your .mdp or in your .top files. Check where you've written Ptotein instead of Protein On 11/25/11 4:09 PM, yp sun wrote: Dear Sir' When I ran the grompp as following grompp -v -f md.mdp -c pr.gro -p RI-10.top -o md.tpr a error information appeared: Program grompp, VERSION 3.3.1 Source code file: readir.c, line: 789 Fatal error: Group Ptotein not found in indexfile Maybe you have non-default goups in your mdp file, while not using the '-n' opti on of grompp. In that case use the '-n' option I don't know which file Group Ptotein is in and where I should make change. Can you help me? Thanks in advance. Yeping Sun CAS Key Laboratory of Pathogenic Microbiology Immunology INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china -- Gianluca Santoni, Institut de Biologie Structurale 41 rue Horowitz Grenoble _ Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html -- 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] grompp error
I think the same with you sir. But I just cann't find where I make this typing error of Ptotein. I checked my md.mdp and RI-10.top and dind't find such a typo. Could you suggest any possible locations of this typo? Yeping Sun CAS Key Laboratory of Pathogenic Microbiology Immunology INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china --- 11年11月25日，周五, Gianluca Santoni gianluca.sant...@ibs.fr 写道： 发件人: Gianluca Santoni gianluca.sant...@ibs.fr 主题: Re: [gmx-users] grompp error 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2011年11月25日,周五,下午4:21 The most reasonable thing is that there is a typo in your .mdp or in your .top files. Check where you've written Ptotein instead of Protein On 11/25/11 4:09 PM, yp sun wrote: Dear Sir' When I ran the grompp as following grompp -v -f md.mdp -c pr.gro -p RI-10.top -o md.tpr a error information appeared: Program grompp, VERSION 3.3.1 Source code file: readir.c, line: 789 Fatal error: Group Ptotein not found in indexfile Maybe you have non-default goups in your mdp file, while not using the '-n' opti on of grompp. In that case use the '-n' option I don't know which file Group Ptotein is in and where I should make change. Can you help me? Thanks in advance. Yeping Sun CAS Key Laboratory of Pathogenic Microbiology Immunology INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china -- Gianluca Santoni, Institut de Biologie Structurale 41 rue Horowitz Grenoble _ Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html -下面为附件内容- -- gmx-users mailing list gmx-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 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] grompp error
Yes I find the in the mdp file I wrote tc-grps=Ptotein Other. Sorry for this stupid error. Thank you. Yeping Sun CAS Key Laboratory of Pathogenic Microbiology Immunology INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china --- 11年11月25日，周五, Gianluca Santoni gianluca.sant...@ibs.fr 写道： 发件人: Gianluca Santoni gianluca.sant...@ibs.fr 主题: Re: [gmx-users] grompp error 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2011年11月25日,周五,下午4:21 The most reasonable thing is that there is a typo in your .mdp or in your .top files. Check where you've written Ptotein instead of Protein On 11/25/11 4:09 PM, yp sun wrote: Dear Sir' When I ran the grompp as following grompp -v -f md.mdp -c pr.gro -p RI-10.top -o md.tpr a error information appeared: Program grompp, VERSION 3.3.1 Source code file: readir.c, line: 789 Fatal error: Group Ptotein not found in indexfile Maybe you have non-default goups in your mdp file, while not using the '-n' opti on of grompp. In that case use the '-n' option I don't know which file Group Ptotein is in and where I should make change. Can you help me? Thanks in advance. Yeping Sun CAS Key Laboratory of Pathogenic Microbiology Immunology INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china -- Gianluca Santoni, Institut de Biologie Structurale 41 rue Horowitz Grenoble _ Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html -下面为附件内容- -- gmx-users mailing list gmx-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 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] grompp line too long error
Here is the detailed info about my setup: System:64-bit Linux GMX version:4.5.4 I know that windows and linux have different line end format and I didn't edit my text files using editor on windows,but all on linux. My goal is to simulate membrane protein embeded in lipid bilayer,I don't have experience working with gromacs before,so I followed the tutorial recommended by the official gromacs website: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html I downloaded the files offered by the tutorial and proceeded and then encountered some problems. As there is no lipid molecular defenition in gromacs,the tutorial refered me to this link: http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies to download the so called Berger lipids,I did exactly what the tutorial instucted. When I called pdb2gmx,I found the nomenclature of atoms in Berger lipids is not consistent with that of the gromos53a6 forcefield. I abandoned Berger lipids because I found the DPPC lipid model offered by Oxford lipidbook is consistent with gromos53a6 forcefield,then pdb2gmx worked.You can find the lipidbook here: http://lipidbook.bioch.ox.ac.uk/package/show/id/14.html After generating the .gro file,I called grompp to generate the .tpr file,and then,grompp throwed the very error message in my original mail.I didn't modify the files generated by the programs I called. In order to re-generate the error message, I zipped the forcefield files I used, you can find it here: http://ishare.iask.sina.com.cn/f/21401866.html?w='%20target='_blank' -- 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] grompp line too long error
Here is the detailed info about my setup: System:64-bit Linux GMX version:4.5.4 I know that windows and linux have different line end format and I didn't edit my text files using editor on windows,but all on linux. Which editor? Problems in principle could arise from your encodings setup, even on linux. My goal is to simulate membrane protein embeded in lipid bilayer,I don't have experience working with gromacs before,so I followed the tutorial recommended by the official gromacs website: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html I downloaded the files offered by the tutorial and proceeded and then encountered some problems. As there is no lipid molecular defenition in gromacs,the tutorial refered me to this link: http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies to download the so called Berger lipids,I did exactly what the tutorial instucted. When I called pdb2gmx,I found the nomenclature of atoms in Berger lipids is not consistent with that of the gromos53a6 forcefield. I abandoned Berger lipids because I found the DPPC lipid model offered by Oxford lipidbook is consistent with gromos53a6 forcefield,then pdb2gmx worked.You can find the lipidbook here: http://lipidbook.bioch.ox.ac.uk/package/show/id/14.html After generating the .gro file,I called grompp to generate the .tpr file,and then,grompp throwed the very error message in my original mail.I didn't modify the files generated by the programs I called. In order to re-generate the error message, I zipped the forcefield files I used, you can find it here: http://ishare.iask.sina.com.cn/f/21401866.html?w='%20target='_blank' http://ishare.iask.sina.com.cn/f/21401866.html?w=%27%20target=%27_blank%27 -- Gianluca Santoni, Institut de Biologie Structurale 41 rue Horowitz Grenoble _ Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html -- 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] grompp line too long error
I was trying to setup a simulation for membrane in DPPC lipid bilayer following this tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html I successfully generated the .gro file for the system.But when I tried grompp to generate the .tpr file,I got the error message shown below: --- Program grompp, VERSION 4.5.4 Source code file: string2.c, line: 105 Fatal error: An input file contains a line longer than 4095 characters, while the buffer passed to fgets2 has size 4095. The line starts with: '20s' For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I use strace to trace the sys call of grompp,I have found that grompp opened gurgle.dat,and ended up reading gurgle.dat as text file,while gurgle.dat is a binary file,then grompp throwed the fatal error message. What could be the cause of this problem? -- 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] grompp line too long error
On 24/11/2011 3:45 PM, 杨伟 wrote: I was trying to setup a simulation for membrane in DPPC lipid bilayer following this tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html I successfully generated the .gro file for the system.But when I tried grompp to generate the .tpr file,I got the error message shown below: --- Program grompp, VERSION 4.5.4 Source code file: string2.c, line: 105 Fatal error: An input file contains a line longer than 4095 characters, while the buffer passed to fgets2 has size 4095. The line starts with: '20s' For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I use strace to trace the sys call of grompp,I have found that grompp opened gurgle.dat,and ended up reading gurgle.dat as text file,while gurgle.dat is a binary file,then grompp throwed the fatal error message. What could be the cause of this problem? I would be more suspicious of your input files than anything else. Make sure you edit them with a sensible text editor that uses useful line endings. Can you use grompp successfully on a simple test case with files you haven't edited? Mark -- 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] grompp line too long error
Hi [insert name here], Try putting an empty gurgle.dat in your working directory to see if that is the problem. If it's not, can you provide additional information regarding your system and gromacs installation? Cheers, Tsjerk On Nov 24, 2011 5:50 AM, 杨伟 20104227...@suda.edu.cn wrote: I was trying to setup a simulation for membrane in DPPC lipid bilayer following this tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html I successfully generated the .gro file for the system.But when I tried grompp to generate the .tpr file,I got the error message shown below: --- Program grompp, VERSION 4.5.4 Source code file: string2.c, line: 105 Fatal error: An input file contains a line longer than 4095 characters, while the buffer passed to fgets2 has size 4095. The line starts with: '20s' For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I use strace to trace the sys call of grompp,I have found that grompp opened gurgle.dat,and ended up reading gurgle.dat as text file,while gurgle.dat is a binary file,then grompp throwed the fatal error message. What could be the cause of this problem? -- 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 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] grompp: invalid bond type error
Hi Justin and Mark, Thank you so much for your replies. Mark, would you mind clarifying what you mean? What exactly should I be looking for in the ffbonded.itp file? I'm not sure why those bonded parameters in particular were overridden... I didn't intend to modify anything! Perhaps it would help if I gave a more complete description of my system. I'm using the oplsaa force field to model a simple alkanethiol chain. I've defined a new residue as follows: [ ALK ] [ atoms ] CA opls_139 -0.180 1 HAA opls_1400.060 1 HAB opls_1400.060 1 HAC opls_1400.060 1 CB opls_139 -0.120 2 HBA opls_1400.060 2 HBB opls_1400.060 2 CC opls_139 -0.120 3 HCA opls_1400.060 3 HCB opls_1400.060 3 CD opls_139 -0.120 4 HDA opls_1400.060 4 HDB opls_1400.060 4 CE opls_139 -0.120 5 HEA opls_1400.060 5 HEB opls_1400.060 5 CF opls_139 -0.120 6 HFA opls_1400.060 6 HFB opls_1400.060 6 CG opls_139 -0.120 7 HGA opls_1400.060 7 HGB opls_1400.060 7 CH opls_139 -0.120 8 HHA opls_1400.060 8 HHB opls_1400.060 8 CI opls_139 -0.120 9 HIA opls_1400.060 9 HIB opls_1400.060 9 CJ opls_139 -0.120 10 HJA opls_1400.060 10 HJB opls_1400.060 10 CK opls_139 -0.120 11 HKA opls_1400.060 11 HKB opls_1400.060 11 CL opls_206 -0.120 12 HLA opls_1400.060 12 HLB opls_1400.060 12 SA opls_200 -0.335 13 HS opls_2040.155 13 [ bonds ] CA HAA CA HAB CA HAC CA CB CB HBA CB HBB CB CC CC HCA CC HCB CC CD CD HDA CD HDB CD CE CE HEA CE HEB CE CF CF HFA CF HFB CF CG CG HGA CG HGB CG CH CH HHA CH HHB CH CI CI HIA CI HIB CI CJ CJ HJA CJ HJB CJ CK CK HKA CK HKB CK CL CL HLA CL HLB CL SA SA HS In ffbonded.itp, I've defined the following bondtypes: ; begin Olivia-defined bondtypes CAHAA 10.10800284512.0 ; spring constant came from OPLS C* HC bondtype CAHAB 10.10800284512.0 CAHAC 10.10800284512.0 CACB 10.15300265265.6 ; spring constant came from OPLS C C3 bondtype CBHBA 10.10800284512.0 CBHBB 10.10800284512.0 CBCC 10.15300265265.6 CCHCA 10.10800284512.0 CCHCB 10.10800284512.0 CCCD 10.15300265265.6 CDHDA 10.10800284512.0 CDHDB 10.10800284512.0 CDCE 10.15300265265.6 CEHEA 10.10800284512.0 CEHEB 10.10800284512.0 CECF 10.15300265265.6 CFHFA 10.10800284512.0 CFHFB 10.10800284512.0 CFCG 10.15300265265.6 CGHGA 10.10800284512.0 CGHGB 10.10800284512.0 CGCH 10.15300265265.6 CHHHA 10.10800284512.0 CHHHB 10.10800284512.0 CHCI 10.15300265265.6 CIHIA 10.10800284512.0 CIHIB 10.10800284512.0 CICJ 10.15300265265.6 CJHJA 10.10800284512.0 CJHJB 10.10800284512.0 CJCK 10.15300265265.6 CKHKA 10.10800284512.0 CKHKB 10.10800284512.0 CKCL 10.15300265265.6 CLHLA 10.10800284512.0 CLHLB 10.10800284512.0 CLSA 10.18200284512.0 ; not sure what the spring constant should be here... will peruse literature! Here is my topology file (different from the last one I posted, since that was for a customized forcefield I had designed from scratch... I have since abandoned that pursuit, and here I am using the predefined opls parameters.) ; Include forcefield parameters #include oplsaa.ff/forcefield.itp [ moleculetype ] ; Namenrexcl Protein 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 1 ALK rtp ALK q -0.2 1 opls_139 1ALK CA 1 -0.18 12.011 ; qtot -0.18 2 opls_140 1ALKHAA 1 0.06 1.008 ; qtot -0.12 3 opls_140 1ALKHAB 1 0.06 1.008 ; qtot -0.06 4 opls_140 1ALKHAC 1 0.06 1.008 ; qtot 0 5 opls_139 1ALK
Re: [gmx-users] grompp: invalid bond type error
Olivia Waring wrote: Hi Justin and Mark, Thank you so much for your replies. Mark, would you mind clarifying what you mean? What exactly should I be looking for in the ffbonded.itp file? I'm not sure why those bonded parameters in particular were overridden... I didn't intend to modify anything! Perhaps it would help if I gave a more complete description of my system. I'm using the oplsaa force field to model a simple alkanethiol chain. I've defined a new residue as follows: [ ALK ] [ atoms ] CA opls_139 -0.180 1 HAA opls_1400.060 1 HAB opls_1400.060 1 HAC opls_1400.060 1 CB opls_139 -0.120 2 HBA opls_1400.060 2 HBB opls_1400.060 2 CC opls_139 -0.120 3 HCA opls_1400.060 3 HCB opls_1400.060 3 CD opls_139 -0.120 4 HDA opls_1400.060 4 HDB opls_1400.060 4 CE opls_139 -0.120 5 HEA opls_1400.060 5 HEB opls_1400.060 5 CF opls_139 -0.120 6 HFA opls_1400.060 6 HFB opls_1400.060 6 CG opls_139 -0.120 7 HGA opls_1400.060 7 HGB opls_1400.060 7 CH opls_139 -0.120 8 HHA opls_1400.060 8 HHB opls_1400.060 8 CI opls_139 -0.120 9 HIA opls_1400.060 9 HIB opls_1400.060 9 CJ opls_139 -0.120 10 HJA opls_1400.060 10 HJB opls_1400.060 10 CK opls_139 -0.120 11 HKA opls_1400.060 11 HKB opls_1400.060 11 CL opls_206 -0.120 12 HLA opls_1400.060 12 HLB opls_1400.060 12 SA opls_200 -0.335 13 HS opls_2040.155 13 [ bonds ] CA HAA CA HAB CA HAC CA CB CB HBA CB HBB CB CC CC HCA CC HCB CC CD CD HDA CD HDB CD CE CE HEA CE HEB CE CF CF HFA CF HFB CF CG CG HGA CG HGB CG CH CH HHA CH HHB CH CI CI HIA CI HIB CI CJ CJ HJA CJ HJB CJ CK CK HKA CK HKB CK CL CL HLA CL HLB CL SA SA HS In ffbonded.itp, I've defined the following bondtypes: ; begin Olivia-defined bondtypes CAHAA 10.10800284512.0 ; spring constant came from OPLS C* HC bondtype CAHAB 10.10800284512.0 CAHAC 10.10800284512.0 CACB 10.15300265265.6 ; spring constant came from OPLS C C3 bondtype CBHBA 10.10800284512.0 CBHBB 10.10800284512.0 CBCC 10.15300265265.6 CCHCA 10.10800284512.0 CCHCB 10.10800284512.0 CCCD 10.15300265265.6 CDHDA 10.10800284512.0 CDHDB 10.10800284512.0 CDCE 10.15300265265.6 CEHEA 10.10800284512.0 CEHEB 10.10800284512.0 CECF 10.15300265265.6 CFHFA 10.10800284512.0 CFHFB 10.10800284512.0 CFCG 10.15300265265.6 CGHGA 10.10800284512.0 CGHGB 10.10800284512.0 CGCH 10.15300265265.6 CHHHA 10.10800284512.0 CHHHB 10.10800284512.0 CHCI 10.15300265265.6 CIHIA 10.10800284512.0 CIHIB 10.10800284512.0 CICJ 10.15300265265.6 CJHJA 10.10800284512.0 CJHJB 10.10800284512.0 CJCK 10.15300265265.6 CKHKA 10.10800284512.0 CKHKB 10.10800284512.0 CKCL 10.15300265265.6 CLHLA 10.10800284512.0 CLHLB 10.10800284512.0 CLSA 10.18200284512.0 ; not sure what the spring constant should be here... will peruse literature! Bond types are not defined by atom name, but rather atom type. If you're using OPLS, then all the types should be opls_* to be valid. I suspect this is at least one source of problem. Here is my topology file (different from the last one I posted, since that was for a customized forcefield I had designed from scratch... I have since abandoned that pursuit, and here I am using the predefined opls parameters.) Does this topology produce the exact same errors as in your last post? -Justin ; Include forcefield parameters #include oplsaa.ff/forcefield.itp [ moleculetype ] ; Namenrexcl Protein 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB ; residue 1 ALK rtp ALK q -0.2 1 opls_139 1ALK CA
Re: [gmx-users] grompp: invalid bond type error
Olivia Waring wrote: Yes, it's the same error. About the bond types: should they be defined as opls_* in ffbonded.itp, aminoacids.rtp, both, or somewhere else entirely? The bonds are named in the aminoacids.rtp file, they are defined in ffbonded.itp. Use names in the .rtp, types in ffbonded.itp. Use existing residues as a guide. -Justin Sorry to be such a nuisance! Olivia On Wed, Nov 2, 2011 at 4:27 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Olivia Waring wrote: Hi Justin and Mark, Thank you so much for your replies. Mark, would you mind clarifying what you mean? What exactly should I be looking for in the ffbonded.itp file? I'm not sure why those bonded parameters in particular were overridden... I didn't intend to modify anything! Perhaps it would help if I gave a more complete description of my system. I'm using the oplsaa force field to model a simple alkanethiol chain. I've defined a new residue as follows: [ ALK ] [ atoms ] CA opls_139 -0.180 1 HAA opls_1400.060 1 HAB opls_1400.060 1 HAC opls_1400.060 1 CB opls_139 -0.120 2 HBA opls_1400.060 2 HBB opls_1400.060 2 CC opls_139 -0.120 3 HCA opls_1400.060 3 HCB opls_1400.060 3 CD opls_139 -0.120 4 HDA opls_1400.060 4 HDB opls_1400.060 4 CE opls_139 -0.120 5 HEA opls_1400.060 5 HEB opls_1400.060 5 CF opls_139 -0.120 6 HFA opls_1400.060 6 HFB opls_1400.060 6 CG opls_139 -0.120 7 HGA opls_1400.060 7 HGB opls_1400.060 7 CH opls_139 -0.120 8 HHA opls_1400.060 8 HHB opls_1400.060 8 CI opls_139 -0.120 9 HIA opls_1400.060 9 HIB opls_1400.060 9 CJ opls_139 -0.120 10 HJA opls_1400.060 10 HJB opls_1400.060 10 CK opls_139 -0.120 11 HKA opls_1400.060 11 HKB opls_1400.060 11 CL opls_206 -0.120 12 HLA opls_1400.060 12 HLB opls_1400.060 12 SA opls_200 -0.335 13 HS opls_2040.155 13 [ bonds ] CA HAA CA HAB CA HAC CA CB CB HBA CB HBB CB CC CC HCA CC HCB CC CD CD HDA CD HDB CD CE CE HEA CE HEB CE CF CF HFA CF HFB CF CG CG HGA CG HGB CG CH CH HHA CH HHB CH CI CI HIA CI HIB CI CJ CJ HJA CJ HJB CJ CK CK HKA CK HKB CK CL CL HLA CL HLB CL SA SA HS In ffbonded.itp, I've defined the following bondtypes: ; begin Olivia-defined bondtypes CAHAA 10.10800284512.0 ; spring constant came from OPLS C* HC bondtype CAHAB 10.10800284512.0 CAHAC 10.10800284512.0 CACB 10.15300265265.6 ; spring constant came from OPLS C C3 bondtype CBHBA 10.10800284512.0 CBHBB 10.10800284512.0 CBCC 10.15300265265.6 CCHCA 10.10800284512.0 CCHCB 10.10800284512.0 CCCD 10.15300265265.6 CDHDA 10.10800284512.0 CDHDB 10.10800284512.0 CDCE 10.15300265265.6 CEHEA 10.10800284512.0 CEHEB 10.10800284512.0 CECF 10.15300265265.6 CFHFA 10.10800284512.0 CFHFB 10.10800284512.0 CFCG 10.15300265265.6 CGHGA 10.10800284512.0 CGHGB 10.10800284512.0 CGCH 10.15300265265.6 CHHHA 10.10800284512.0 CHHHB 10.10800284512.0 CHCI 10.15300265265.6 CIHIA 10.10800284512.0 CIHIB 1
[gmx-users] grompp: invalid bond type error
Dear Gromacs users, First of all, many thanks to Justin for his assistance with my previous question. I have defined a new residue type in the oplsaa force field, changing the aminoacids.rtp file accordingly. pdb2gmx worked just fine; but when I try to preprocess, I get the following output: WARNING 1 [file ffbonded.itp, line 58]: Overriding Bond parameters. old: 0.1229 476976 0.1229 476976 new: C O 10.13270 179075.2 WARNING 2 [file ffbonded.itp, line 64]: Overriding Bond parameters. old: 0.1522 265266 0.1522 265266 new: CCT 10.14950 265265.6 WARNING 3 [file ffbonded.itp, line 67]: Overriding Bond parameters. old: 0.149 334720 0.149 334720 new: CAC 10.14240 392459.2 WARNING 4 [file ffbonded.itp, line 73]: Overriding Bond parameters. old: 0.1419 374050 0.1419 374050 new: CCB 10.14240 392459.2 --- Program grompp, VERSION 4.5.4 Source code file: topdirs.c, line: 76 Fatal error: Invalid bond type 0 For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors The error is rather cryptic, and I'm having trouble tracking it down... I even went to the source code (topdirs.c), but I'm still not sure where exactly this invalid bond type is being defined. Thank you so much for your help, Olivia -- Olivia Waring (王维娅) Princeton University '12 AB Chemistry -- 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
