Hi, That tends to suggest either your ligand conformation or ligand parameters are not appropriate. What happens with ligand in vacuo with EM and then NVE with a very small time step, e.g. 0.00005 ps?
Mark On Sat, Nov 10, 2018 at 10:50 AM Farial Tavakoli <faryal.tavak...@gmail.com> wrote: > Dear gromacs users > > I am trying to simulate a complex, including a protein and a peptidec > ligand with 2 phosphotyrosine residues. > The protein topology was generated using amber99sb.ff in gromacs and the > ligand topology was generated using ff99sb in amber tools 16, then the > .inpcrd and .prmtop files were converted to .gmx and .top files using > acpype python script. > *python acpype.py -p prmtop -x inpcrd* > .itp file was created by removing header and footer of .top file. > Then .gro and .top files were modified according to the tutorial in > gromacs. > I tryed to minimize the complex , but it stoped before 100 steps : > > > > > > *Steepest Descents converged to machine precision in 80 steps,but did not > reach the requested Fmax < 1000.Potential Energy = -6.5639856e+05Maximum > force = 7.0647156e+04 on atom 5256Norm of force = 5.8775842e+02* > > and when I run NVT simulation , faced to LINCS warning: > > > > > > > > > > > *starting mdrun 'Protein in water'200000 steps, 400.0 ps.step 0Step 5, > time 0.01 (ps) LINCS WARNINGrelative constraint deviation after LINCS:rms > 0.016999, max 0.734404 (between atoms 5258 and 5261)bonds that rotated more > than 30 degrees: atom 1 atom 2 angle previous, current, constraint > length 5258 5261 90.0 0.0960 0.1665 0.0960 5283 5286 > 90.0 0.0960 0.1425 0.0960Wrote pdb files with previous and > current coordinates* > I separated my complex in to protein and ligand and simulated the protein > alone in the TIP3P water model. that was stable. then, simulated the ligand > in vacuo and faced with LINCS warning. > Both force fields that were used to generate topologies were AMBER99sb, Is > it possible its because of .mdp files which I used? > Would you please reply and advice me how I can resolve this problem? > > best regards > Farial > > the em.mdp file: > ; minim.mdp - used as input into grompp to generate em.tpr > integrator = steep > emtol = 1000.0 > emstep = 0.01 > nsteps = 50000 > nstlist = 1 > cutoff-scheme = Verlet > ns_type = grid > coulombtype = PME > rcoulomb = 1.0 > rvdw = 1.0 > pbc = xyz > > nvt.mdp file: > title = AMBER NVT equilibration > define = -DPOSRES ; position restrain the protein > ; Run parameters > integrator = md > nsteps = 200000 ; 2 * 200000 = 400 ps > dt = 0.002 > ; Output control > nstxout = 500 > nstvout = 500 > nstenergy = 500 > nstlog = 500 > ; Bond parameters > continuation = no > constraint_algorithm = lincs > constraints = h-bonds > lincs_iter = 1 > lincs_order = 4 > ; Nonbonded settings > cutoff-scheme = Verlet > ns_type = grid > nstlist = 10 > rcoulomb = 1.0 > rvdw = 1.0 > ; Electrostatics > coulombtype = PME > pme_order = 4 > fourierspacing = 0.16 > ; Temperature coupling is on > tcoupl = V-rescale > tc-grps = Protein Non-Protein > tau_t = 0.1 0.1 > ref_t = 300 300 > ; Pressure coupling is off > pcoupl = no > ; Periodic boundary conditions > pbc = xyz > ; Velocity generation > gen_vel = yes > gen_temp = 300 > gen_seed = -1 > -- > 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. > -- 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.