hi Justin, Thanks, that makes sense, however I was able to use the same ligand toplogy files with earlier versions like gromacs 4.5.4 to simulate protein ligand complexes. I can simulate protein-ligand complexes with the current versions also but only for the crystal structures that have ligand bound to it, not the modelled proteins with ligands bound.
and also I would appreciate any comments on the mdp file as below: title = Bilayer-500 cpp = /lib/cpp constraint_algorithm = lincs constraints = all-bonds; added lincs_iter = 1; added lincs_order = 4; added integrator = md; dt = 0.002 tinit = 0; nsteps = 1000000 ; 2 ns nstcomm = 500 nstxout = 5000 nstvout = 5000 nstfout = 0 nstxtcout = 500 xtc_precision = 1000 nstlog = 500 nstenergy = 500 nstlist = 50 ns_type = grid; added nstcalclr = 1 ; long range interactions coulombtype = PME rlist = 1.4 rcoulomb = 1.2 rvdw = 1.2 fourierspacing = 0.16 pme_order = 4 vdw-type = Cut-off cutoff-scheme = Verlet Tcoupl = v-rescale tau_t = 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 tc-grps = Protein POP SOL NA CL LIG SOD CLA ref_t = 303 303 303 303 303 303 303 303 ; Energy monitoring energygrps = Protein POP SOL SOD CLA LIG NA CL Pcoupl = Berendsen pcoupltype = semiisotropic tau_p = 1.0 1.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 DispCorr = no ; added ;generate velocites is on at 293K gen_vel = yes gen_temp = 303.0 gen_seed = 478905 comm-mode = Linear comm-grps = System Thanks, Pramod On Mon, Jun 23, 2014 at 8:03 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 6/23/14, 5:53 PM, ram bio wrote: > >> Dear Gromacs Users, >> >> I have been trying to simulate protein-ligand complex using gromacs >> versions that use verlet cutoff scheme on gpus. >> >> These are some of the issues that i could resolve, and any kind of >> suggestion or help is appreciated. >> >> 1. With gromacs 4.6.5 i could simulate crystal structure from pdb but not >> modelled protein with ligand always ended up in segmentation fault. The MD >> run during equillibration runs for gew thousands of steps and errors out >> as >> segmentation fault, so i have to rerun using previous cpt file, for a run >> of 2ns to complete i have to rerun it for 7-10 times. >> >> So if the the system id not minimized, why would it go into rerun? >> >> 2. I though it could be a bug and used 4.6.3 and 5.0 release, with this >> trial i could equillibrate just modelled protein but not with the >> protein-ligand complex. The same error occurs as i mentioned above with >> protein-ligand complex... >> >> I am attaching my mdp file and the minimized structure that i am using for >> equillibration. >> >> > The list doesn't accept attachments. > > It seems clear to me that your ligand topology is not stable. If the > protein works, but the protein+ligand doesn't, what's changing? That's the > likeliest source of your problem. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA 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 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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.
