[gmx-users] adding metal ion
hello users I need to add selenium ion in the protein complex. Can anyone tell me how to add a metal ion in gromacs? I posted the question before but I didn't get any reply so I am posting again. Please tell me if anybody knows. -- 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] gromacs
hello users Can anyone tell me that is it necessary to run a long simulation at one tme? or I can do it in parts. Like if i am doing for 1000ps, can i do 500 at one tme and rest in next run? Would it give same results or its a wrong procedure? -- 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] md simulation steps
hello Can you tell me how many steps are sufficient for md simulation of protein-ligand complex? -- 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] too many lincs warnings
Thanks.. On Aug 20, 2014 1:29 PM, Meenakshi Rajput ashi.rajpu...@gmail.com wrote: hello users I had done energy minimisation of protein-ligand complex and i got negative potential. Also the ligand was at right place after EM run but when I tried the positional restrained run, too many lincs warnings came and md run stopped suddenly. I am using charmm force field and mdp file settings for position restrined run are:- 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= 500; save coordinates every 0.2 ps nstvout= 500; save velocities every 0.2 ps nstenergy= 500; save energies every 0.2 ps nstlog= 500; update log file every 0.2 ps ; Bond parameters continuation= yes; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching cutoff-scheme = Verlet ns_type= grid; search neighboring grid cells nstlist= 10; 10 fs rlist= 1.2; short-range neighborlist cutoff (in nm) rcoulomb= 1.2; short-range electrostatic cutoff (in nm) rvdw= 1.2; short-range van der Waals cutoff (in nm) rvdw-switch = 1.0 ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= Protein Non-Protein; two coupling groups - more accurate tau_t= 0.10.1; 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 Please tell me if there is something wrong with mdp settings or is it some other problem? -- 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] too many lincs warnings
hello users I had done energy minimisation of protein-ligand complex and i got negative potential. Also the ligand was at right place after EM run but when I tried the positional restrained run, too many lincs warnings came and md run stopped suddenly. I am using charmm force field and mdp file settings for position restrined run are:- 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= 500; save coordinates every 0.2 ps nstvout= 500; save velocities every 0.2 ps nstenergy= 500; save energies every 0.2 ps nstlog= 500; update log file every 0.2 ps ; Bond parameters continuation= yes; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching cutoff-scheme = Verlet ns_type= grid; search neighboring grid cells nstlist= 10; 10 fs rlist= 1.2; short-range neighborlist cutoff (in nm) rcoulomb= 1.2; short-range electrostatic cutoff (in nm) rvdw= 1.2; short-range van der Waals cutoff (in nm) rvdw-switch = 1.0 ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= Protein Non-Protein; two coupling groups - more accurate tau_t= 0.10.1; 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 Please tell me if there is something wrong with mdp settings or is it some other problem? -- 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] potential energy
Thanks a lot Justin. On Aug 11, 2014 10:36 PM, Meenakshi Rajput ashi.rajpu...@gmail.com wrote: thanks...can you help me out with the mdp file settings with charmm force field(proteins)? I am a new user to gromacs and stuck here. On Mon, Aug 11, 2014 at 5:07 AM, Meenakshi Rajput ashi.rajpu...@gmail.com wrote: Thanks..but if potential becomes positive after energy minimisation run, then is it normal or there is some prblm with my mdp file. I used the same mdp file for this run also. I used charmm force field. On Aug 11, 2014 2:32 PM, Meenakshi Rajput ashi.rajpu...@gmail.com wrote: hi users i have run energy minimisation of docked complex by using this min.mdp:- cpp= /lib/cpp; Preprocessor include= -I../top; Directories to include in the topology format integrator= steep emtol= 1000; Stop minimization when the energy changes by less than emtol kJ/mol. nsteps= 200; Maximum number of (minimization) steps to perform nstenergy= 10; Write energies to disk every nstenergy steps nstxtcout= 10; Write coordinates to disk every nstxtcout steps xtc_grps= Protein; Which coordinate group(s) to write to disk energygrps= Protein; Which energy group(s) to write to disk nstlist= 5; 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; long range electrostatic cut-off rvdw= 1.2; long range Van der Waals cut-off constraints= none; Bond types to replace by constraints pbc= xyz; Periodic Boundary Conditions (yes/no0 After the run, potential energy is negative. can you tell me whats the problem?? -- 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] potential energy
hi thanks for the charmm settings...but N atom and H atom of LYS 313 and ALA 364 are coming out of the complex. Can you tell me why is this happening? And in next positional restrained run and md simulation, charmm settings would be same or some difference should be there? On Tue, Aug 12, 2014 at 10:33 PM, Meenakshi Rajput ashi.rajpu...@gmail.com wrote: Thanks a lot Justin. On Aug 11, 2014 10:36 PM, Meenakshi Rajput ashi.rajpu...@gmail.com wrote: thanks...can you help me out with the mdp file settings with charmm force field(proteins)? I am a new user to gromacs and stuck here. On Mon, Aug 11, 2014 at 5:07 AM, Meenakshi Rajput ashi.rajpu...@gmail.com wrote: Thanks..but if potential becomes positive after energy minimisation run, then is it normal or there is some prblm with my mdp file. I used the same mdp file for this run also. I used charmm force field. On Aug 11, 2014 2:32 PM, Meenakshi Rajput ashi.rajpu...@gmail.com wrote: hi users i have run energy minimisation of docked complex by using this min.mdp:- cpp= /lib/cpp; Preprocessor include= -I../top; Directories to include in the topology format integrator= steep emtol= 1000; Stop minimization when the energy changes by less than emtol kJ/mol. nsteps= 200; Maximum number of (minimization) steps to perform nstenergy= 10; Write energies to disk every nstenergy steps nstxtcout= 10; Write coordinates to disk every nstxtcout steps xtc_grps= Protein; Which coordinate group(s) to write to disk energygrps= Protein; Which energy group(s) to write to disk nstlist= 5; 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; long range electrostatic cut-off rvdw= 1.2; long range Van der Waals cut-off constraints= none; Bond types to replace by constraints pbc= xyz; Periodic Boundary Conditions (yes/no0 After the run, potential energy is negative. can you tell me whats the problem?? -- 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] potential energy
hi users i have run energy minimisation of docked complex by using this min.mdp:- cpp= /lib/cpp; Preprocessor include= -I../top; Directories to include in the topology format integrator= steep emtol= 1000; Stop minimization when the energy changes by less than emtol kJ/mol. nsteps= 200; Maximum number of (minimization) steps to perform nstenergy= 10; Write energies to disk every nstenergy steps nstxtcout= 10; Write coordinates to disk every nstxtcout steps xtc_grps= Protein; Which coordinate group(s) to write to disk energygrps= Protein; Which energy group(s) to write to disk nstlist= 5; 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; long range electrostatic cut-off rvdw= 1.2; long range Van der Waals cut-off constraints= none; Bond types to replace by constraints pbc= xyz; Periodic Boundary Conditions (yes/no0 After the run, potential energy is negative. can you tell me whats the problem?? -- 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] potential energy
Thanks..but if potential becomes positive after energy minimisation run, then is it normal or there is some prblm with my mdp file. I used the same mdp file for this run also. I used charmm force field. On Aug 11, 2014 2:32 PM, Meenakshi Rajput ashi.rajpu...@gmail.com wrote: hi users i have run energy minimisation of docked complex by using this min.mdp:- cpp= /lib/cpp; Preprocessor include= -I../top; Directories to include in the topology format integrator= steep emtol= 1000; Stop minimization when the energy changes by less than emtol kJ/mol. nsteps= 200; Maximum number of (minimization) steps to perform nstenergy= 10; Write energies to disk every nstenergy steps nstxtcout= 10; Write coordinates to disk every nstxtcout steps xtc_grps= Protein; Which coordinate group(s) to write to disk energygrps= Protein; Which energy group(s) to write to disk nstlist= 5; 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; long range electrostatic cut-off rvdw= 1.2; long range Van der Waals cut-off constraints= none; Bond types to replace by constraints pbc= xyz; Periodic Boundary Conditions (yes/no0 After the run, potential energy is negative. can you tell me whats the problem?? -- 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] potential energy
thanks...can you help me out with the mdp file settings with charmm force field(proteins)? I am a new user to gromacs and stuck here. On Mon, Aug 11, 2014 at 5:07 AM, Meenakshi Rajput ashi.rajpu...@gmail.com wrote: Thanks..but if potential becomes positive after energy minimisation run, then is it normal or there is some prblm with my mdp file. I used the same mdp file for this run also. I used charmm force field. On Aug 11, 2014 2:32 PM, Meenakshi Rajput ashi.rajpu...@gmail.com wrote: hi users i have run energy minimisation of docked complex by using this min.mdp:- cpp= /lib/cpp; Preprocessor include= -I../top; Directories to include in the topology format integrator= steep emtol= 1000; Stop minimization when the energy changes by less than emtol kJ/mol. nsteps= 200; Maximum number of (minimization) steps to perform nstenergy= 10; Write energies to disk every nstenergy steps nstxtcout= 10; Write coordinates to disk every nstxtcout steps xtc_grps= Protein; Which coordinate group(s) to write to disk energygrps= Protein; Which energy group(s) to write to disk nstlist= 5; 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; long range electrostatic cut-off rvdw= 1.2; long range Van der Waals cut-off constraints= none; Bond types to replace by constraints pbc= xyz; Periodic Boundary Conditions (yes/no0 After the run, potential energy is negative. can you tell me whats the problem?? -- 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] ligand binding
hello I have used charmm27 force field to parametrize my protein(human serum albumin,584a.a) and swiss param to provide parameters to the ligand due to which coordinates of ligand is changed and active site of protein is also completely changed. Can anybody tell me that ligand coordinates should be changed after parametrization? or any energy minimisation problem is there. Am i doing right or not? My energy minimization mdp file is here:- cpp= /lib/cpp include= -I../top integrator= steep emtol= 100 nsteps= 200 nstenergy= 10 nstxtcout= 10 xtc_grps= Protein energygrps= Protein nstlist= 5 ns_type= grid rlist= 1.4 coulombtype= PME rcoulomb= 1.4 rvdw= 1.4 constraints= none pbc= xyz Energy is not reached upto mentioned limit after EM run. -- 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] gromacs
hi gromacs users I have done the whole mdrun simulation of my protein human serum albumin complex with ligand and i got all the files. But when i opened the pdb file obtained after md simulation in pymol to see the interaction, ligand went to some other place. It was not in the active site. please tell me what is the problem, where i m wrong? -- 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] grompp
Hi gromacs users I run the grompp command (grompp_d -v -f minim.mdp -c sol.gro -o min.tpr -p hsa.top) to generate .tpr file but i got the following error Fatal error: number of coordinates in coordinate file (sol.gro, 140012) does not match topology (hsa.top, 140027) When I opened gro file, only protein and sol molecules are seen in .gro file but no ligand molecules. I dont know why it is happening.. Can anybody help me? -- 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] grompp
Hi I have made my ligand coordinate file using prodrg server. And the 15 missing atoms are the ligand atoms as they are not seen in gro file. I have modified protein's topology file. Is there any change i have to make in gro file except adding ligand coordinates? -- 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
dear gromacs users I tried mdrun in gromacs but *it stopped in between and showing the fallowing error * *:-**Segmentation fault (Core dumped) * *Can any one please tell what is the problem and how to solve it? * -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] (no subject)
I tried to do perform mdrun on myo.pdb by using command g_mdrun -v -s m.tpr -o minim_traj.trr -c myo.gro -e minim_ener.edr. But I got the following error:- Reading file m.tpr, VERSION 4.6.5 (single precision) Using 1 MPI thread WARNING: Oversubscribing the available 0 logical CPU cores with 1 thread-MPI threads. This will cause considerable performance loss! Segmentation fault (core dumped) -- 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] gromacs
i used the pdb2gmx command but i get a message command not found. can you help me -- 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] about gromacs
hi..i have installed rpm version of gromacs on my machine with core i3 processor. Can you send me the command list of gromacs. -- 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.
