Re: [gmx-users] Segmentation fault (core dumped) error during minimization
On 4/28/20 5:08 AM, Elham Taghikhani wrote: Hi As you said I checked my structure for any bad contact, but the close atoms are part of the protein so I can't delete them to minimize the structure. And water molecules are not that much close to make bad contact with the atom. And the atom which errored during minimization it's the atom that bound covalently to a ligand. I think there is something wrong with the bond length between N of amino acid and the C of the ligand. How can I find the correct bond length? You'll have to provide more information about how you parametrized this covalent ligand. This is a far different case from a "normal" protein-ligand complex and requires very careful force field parametrization, including the linkage itself and any impacts that may have on associated protein terms. In this case, I don't see how you can assess the stability of the ligand topology by itself, as you said you had. Please explain in greater detail. -Justin On Apr 20, 2020, at 1:08 AM, Elham Taghikhani wrote: Thank you I corrected the mdp file. As you said I opened my gro file in VMD but I didn't notice any bad contact around the atom. Could you explain how can I observe bad contacts in the structure? I even tried the different box size but it didn't work. Both ligand and protein are ok with minimization separately. On Apr 19, 2020, at 11:13 PM, Elham Taghikhani wrote: Hi I am simulating a protein-ligand system, using oplss force field but i got this error during minimization. Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=5 Step=0, Dmax= 1.0e-02 nm, Epot= 1.27151e+33 Fmax= 4.76291e+07, atom= 1996 Segmentation fault (core dumped) and this is my mpd file: ; LINES STARTING WITH ';' ARE COMMENTS title = Minimization ; Title of run ; 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 < 10.0 kJ/mol 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 and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet 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 ; long range electrostatic cut-off vdwtype = cutoff vdw-modifier= force-switch rvdw-switch = 1.0 rvdw= 1.2 ; long range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions DispCorr= no Can anyone suggest how to troubleshoot this error? The system is nuetralized. Thank you in advance. -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Segmentation fault (core dumped) error during minimization
Hi As you said I checked my structure for any bad contact, but the close atoms are part of the protein so I can't delete them to minimize the structure. And water molecules are not that much close to make bad contact with the atom. And the atom which errored during minimization it's the atom that bound covalently to a ligand. I think there is something wrong with the bond length between N of amino acid and the C of the ligand. How can I find the correct bond length? > On Apr 20, 2020, at 1:08 AM, Elham Taghikhani wrote: > > Thank you > I corrected the mdp file. As you said I opened my gro file in VMD but I > didn't notice any bad contact around the atom. > Could you explain how can I observe bad contacts in the structure? > I even tried the different box size but it didn't work. > Both ligand and protein are ok with minimization separately. > > >>> On Apr 19, 2020, at 11:13 PM, Elham Taghikhani >>> wrote: >>> >> >> Hi >> >> I am simulating a protein-ligand system, using oplss force field but i got >> this error during minimization. >> >> Steepest Descents: >>Tolerance (Fmax) = 1.0e+03 >>Number of steps=5 >> Step=0, Dmax= 1.0e-02 nm, Epot= 1.27151e+33 Fmax= 4.76291e+07, atom= >> 1996 >> Segmentation fault (core dumped) >> >> and this is my mpd file: >> ; LINES STARTING WITH ';' ARE COMMENTS >> title= Minimization ; Title of run >> >> ; 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 < 10.0 kJ/mol >> 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 and how to >> calculate the interactions >> nstlist = 1 ; Frequency to update the >> neighbor list and long range forces >> cutoff-scheme = Verlet >> 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 ; long range electrostatic cut-off >> vdwtype = cutoff >> vdw-modifier= force-switch >> rvdw-switch = 1.0 >> rvdw = 1.2 ; long range Van der Waals cut-off >> pbc = xyz; Periodic Boundary Conditions >> DispCorr= no >> Can anyone suggest how to troubleshoot this error? >> The system is nuetralized. >> >> Thank you in advance. >> -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Segmentation fault (core dumped) error during minimization
On 4/19/20 4:38 PM, Elham Taghikhani wrote: Thank you I corrected the mdp file. As you said I opened my gro file in VMD but I didn't notice any bad contact around the atom. Could you explain how can I observe bad contacts in the structure? Calculate interatomic distances and look for anything very close to atom 1996, check the topology to make sure sensible interactions will occur between that atom and its surroundings. I even tried the different box size but it didn't work. Box size is not relevant here. -Justin Both ligand and protein are ok with minimization separately. On Apr 19, 2020, at 11:13 PM, Elham Taghikhani wrote: Hi I am simulating a protein-ligand system, using oplss force field but i got this error during minimization. Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=5 Step=0, Dmax= 1.0e-02 nm, Epot= 1.27151e+33 Fmax= 4.76291e+07, atom= 1996 Segmentation fault (core dumped) and this is my mpd file: ; LINES STARTING WITH ';' ARE COMMENTS title = Minimization ; Title of run ; 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 < 10.0 kJ/mol 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 and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet 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 ; long range electrostatic cut-off vdwtype = cutoff vdw-modifier= force-switch rvdw-switch = 1.0 rvdw= 1.2 ; long range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions DispCorr= no Can anyone suggest how to troubleshoot this error? The system is nuetralized. Thank you in advance. -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Segmentation fault (core dumped) error during minimization
Thank you I corrected the mdp file. As you said I opened my gro file in VMD but I didn't notice any bad contact around the atom. Could you explain how can I observe bad contacts in the structure? I even tried the different box size but it didn't work. Both ligand and protein are ok with minimization separately. > On Apr 19, 2020, at 11:13 PM, Elham Taghikhani wrote: > > > Hi > > I am simulating a protein-ligand system, using oplss force field but i got > this error during minimization. > > Steepest Descents: >Tolerance (Fmax) = 1.0e+03 >Number of steps=5 > Step=0, Dmax= 1.0e-02 nm, Epot= 1.27151e+33 Fmax= 4.76291e+07, atom= 1996 > Segmentation fault (core dumped) > > and this is my mpd file: > ; LINES STARTING WITH ';' ARE COMMENTS > title = Minimization ; Title of run > > ; 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 < > 10.0 kJ/mol > 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 and how to > calculate the interactions > nstlist = 1 ; Frequency to update the > neighbor list and long range forces > cutoff-scheme = Verlet > 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 ; long range electrostatic cut-off > vdwtype = cutoff > vdw-modifier= force-switch > rvdw-switch = 1.0 > rvdw = 1.2 ; long range Van der Waals cut-off > pbc = xyz ; Periodic Boundary Conditions > DispCorr= no > Can anyone suggest how to troubleshoot this error? > The system is nuetralized. > > Thank you in advance. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Segmentation fault (core dumped) error during minimization
On 4/19/20 2:43 PM, Elham Taghikhani wrote: Hi I am simulating a protein-ligand system, using oplss force field but i got this error during minimization. Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps = 5 Step= 0, Dmax= 1.0e-02 nm, Epot= 1.27151e+33 Fmax= 4.76291e+07, atom= 1996 Look for bad contacts around atom 1996. Segmentation fault (core dumped) and this is my mpd file:; LINES STARTING WITH ';' ARE COMMENTS title = Minimization ; Title of run ; 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 < 10.0 kJ/mol 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 and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet 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 ; long range electrostatic cut-off vdwtype = cutoff vdw-modifier= force-switch rvdw-switch = 1.0 rvdw= 1.2 ; long range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions DispCorr= no Can anyone suggest how to troubleshoot this error? Your cutoffs are for the CHARMM force field, not OPLS. This isn't the source of the error, but you are using the force field incorrectly. Other than that, protein-ligand complexes are specifically addressed in the troubleshooting section of http://manual.gromacs.org/current/user-guide/terminology.html#diagnosing-an-unstable-system -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Segmentation fault (core dumped) error during minimization
Hi I am simulating a protein-ligand system, using oplss force field but i got this error during minimization. Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps = 5 Step= 0, Dmax= 1.0e-02 nm, Epot= 1.27151e+33 Fmax= 4.76291e+07, atom= 1996 Segmentation fault (core dumped) and this is my mpd file:; LINES STARTING WITH ';' ARE COMMENTS title = Minimization ; Title of run ; 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 < 10.0 kJ/mol 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 and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet 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 ; long range electrostatic cut-off vdwtype = cutoff vdw-modifier= force-switch rvdw-switch = 1.0 rvdw= 1.2 ; long range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions DispCorr= no Can anyone suggest how to troubleshoot this error? The system is nuetralized. Thank you in advance. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
