Hi, I am trying to calculate ligand binding affinity of Dimeric Protein(198 residues) complexed with a peptide(3 residues) using Linear Interaction Energy method.The water box dimensions of ligand with protein and Ligand in water are considered to be same. I am encountering problem in estimating long range electrostatic interactions for ligand interacting with solvent. I have used PME for coulomb-type (trajectory length is 1ns) The option I used in g_energy to extract long range electrostatic interactions is Coul-Recip and results appear to be strange since,the electrostatic energy(EE for ligand in solvent are more negative than electrostatic for ligand in protein, which implies positive values for delta EE(quite weird!) I just wanted to know what are the proper mdp options in order to get meaningful results and also what is the option in g_energy to get LR interactions, whether usage of Coul-Recip is correct or not? I also want to know the cutoffs to be mentioned in order to calculate SR and LR. Whether I should be using Reaction Field or cut-off for treatment of LR interactions The mdp file which I have been using is attached below title = Protein-Peptide Complex ; Run parameters integrator = md ; leap-frog integrator nsteps = 500000 ; 2 * 500000 = 1000 ps, 1 ns dt = 0.002 ; 2 fs ; Output control nstxout = 1000 ; save coordinates every 2 ps nstvout = 1000 ; save velocities every 2 ps nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps ; Bond parameters continuation = yes ; Restarting after NPT 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 ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 0.5 ; short-range neighborlist cutoff (in nm) rcoulomb = 0.5 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) ; 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 = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 pbc = xyz ; 3-D PBC DispCorr = EnerPres ; account for cut-off vdW scheme gen_vel = no ; Velocity generation is off
Many thanks in advance for your attention. I'd appreciate any help in this regard. Regards, Hindu Tera -- 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
