Ok..I got it Thanks Justin...
--Rama On Mon, Sep 9, 2013 at 1:49 PM, Rama Krishna Koppisetti < ramkishn...@gmail.com> wrote: > > Hi Justin , > > I prepared .rtp files for lipid. what is the exact command to merge two > chains in gromacs. > > > > > On Fri, Sep 6, 2013 at 4:37 PM, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 9/6/13 5:35 PM, Rama Krishna Koppisetti wrote: >> >>> H >>> i Justin, >>> >>> Thanks for your reply. >>> >>> >>> How to do that? >>> >>> >> If .rtp entries exist for your lipid with the force field, it's simply a >> matter of pdb2gmx -merge, choosing which chains should be written as a >> single [moleculetype]. If the lipids are not described by .rtp entries, >> you either have to write one or modify the topology by hand (ugh) or with >> some script. >> >> -Justin >> >> >>> >>> On Fri, Sep 6, 2013 at 4:27 PM, Justin Lemkul <jalem...@vt.edu> wrote: >>> >>> >>>> >>>> On 9/6/13 5:23 PM, Rama wrote: >>>> >>>> Hi, >>>>> >>>>> I'm doing NMR restrained MD simulation for protein-Bilayer system to >>>>> satisfy >>>>> NMR experimental data. >>>>> >>>>> Without restraints there is no problem, but if I include distance >>>>> restraints >>>>> in topology file, getting fatal error: >>>>> >>>>> the lipid atom index # was not recognized by using this command: >>>>> g_grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx >>>>> -o >>>>> md.tpr -maxwarn 5 >>>>> >>>>> even in index file protein_DMPC atoms index is there continuously. Any >>>>> one >>>>> have suggestions to overcome this fatal error. Thanks >>>>> >>>>> / >>>>> [ file beta_disres.itp, line 4 ]: >>>>> Atom index (2679) in distance_restraints out of bounds (1-2513)./ >>>>> >>>>> >>>>> Just like position restraints, distance restraints only work within a >>>> [moleculetype]. Thus you're probably trying to restrain atoms between >>>> [moleculetype] directives, which does not work. You could theoretically >>>> make a merged [moleculetype] of whatever species need to be restrained, >>>> but >>>> that may take a bit of effort depending on what is being restrained. >>>> >>>> -Justin >>>> >>>> >>>> md.mdp file: >>>> >>>>> title = protein-bilayer complex >>>>> define = -DDISRES ; NMR Distance restraints >>>>> ; Run parameters >>>>> integrator = md ; leap-frog integrator >>>>> nsteps = 2500000 ; >>>>> dt = 0.002 ; 2 fs >>>>> ; Output control >>>>> nstxout = 5000 ; save coordinates every 5 ps >>>>> nstvout = 5000 ; save velocities every 5 ps >>>>> nstxtcout = 5000 ; xtc compressed trajectory output >>>>> every >>>>> 5 ps >>>>> nstenergy = 5000 ; save energies every 5 ps >>>>> nstlog = 5000 ; update log file every 5 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 >>>>> ; Distance restraints parameters >>>>> disre = simple ; simple (per-molecule) >>>>> disre_fc = 1000 ; force constant for distance >>>>> restraints >>>>> ; Neighborsearching >>>>> ns_type = grid ; search neighboring grid cels >>>>> nstlist = 5 ; 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) >>>>> ; 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 = Nose-Hoover ; More accurate thermostat >>>>> tc-grps = Protein non-protein non-protein ; three >>>>> coupling groups - >>>>> more accurate >>>>> tau_t = 0.5 0.5 0.5 ; time >>>>> constant, >>>>> in ps >>>>> ref_t = 303 303 303 ; reference >>>>> temperature, one for >>>>> each group, in K >>>>> ; Pressure coupling is on >>>>> pcoupl = Parrinello-Rahman ; Pressure coupling on in >>>>> NPT >>>>> pcoupltype = semiisotropic ; uniform scaling of x-y >>>>> box >>>>> vectors, >>>>> independent z >>>>> tau_p = 2.0 ; time constant, in ps >>>>> ref_p = 1.0 1.0 ; reference pressure, >>>>> x-y, z (in bar) >>>>> compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, >>>>> bar^-1 >>>>> ; Periodic boundary conditions >>>>> pbc = xyz ; 3-D PBC >>>>> ; Dispersion correction >>>>> DispCorr = EnerPres ; account for cut-off vdW scheme >>>>> ; Velocity generation >>>>> gen_vel = no ; Velocity generation is off >>>>> ; COM motion removal >>>>> ; These options remove motion of the protein/bilayer relative to the >>>>> solvent/ions >>>>> nstcomm = 1 >>>>> comm-mode = Linear >>>>> comm-grps = protein non-protein >>>>> >>>>> topology file: >>>>> >>>>> >>>>> ; Include Position restraint file >>>>> #ifdef POSRES >>>>> #include "posre.itp" >>>>> #endif >>>>> >>>>> ; Include Distance restraints file >>>>> #ifdef DISRES >>>>> #include "beta_disres.itp" >>>>> #endif >>>>> >>>>> ; Strong position restraints for InflateGRO >>>>> #ifdef STRONG_POSRES >>>>> #include "strong_posre.itp" >>>>> #endif >>>>> >>>>> ; Include DMPC topology >>>>> #include "ramaLJ.ff/dmpcLJ.itp" >>>>> >>>>> ; Include water topology >>>>> #include "ramaLJ.ff/spc.itp" >>>>> >>>>> #ifdef POSRES_WATER >>>>> ; Position restraint for each water oxygen >>>>> [ position_restraints ] >>>>> ; i funct fcx fcy fcz >>>>> 1 1 1000 1000 1000 >>>>> #endif >>>>> >>>>> ; Include topology for ions >>>>> #include "ramaLJ.ff/ions.itp" >>>>> >>>>> [ system ] >>>>> ; Name >>>>> Giving Russians Opium May Alter Current Situation in water >>>>> >>>>> [ molecules ] >>>>> ; Compound #mols >>>>> Protein 1 >>>>> DMPC 125 >>>>> SOL 8335 >>>>> CL 8 >>>>> >>>>> >>>>> >>>>> -- >>>>> View this message in context: http://gromacs.5086.x6.nabble.**** >>>>> com/NMR-restrained-MD-****tp5011025.html<http://gromacs.** >>>>> 5086.x6.nabble.com/NMR-**restrained-MD-tp5011025.html<http://gromacs.5086.x6.nabble.com/NMR-restrained-MD-tp5011025.html> >>>>> > >>>>> >>>>> Sent from the GROMACS Users Forum mailing list archive at Nabble.com. >>>>> >>>>> >>>>> -- >>>> ==============================****==================== >>>> >>>> >>>> Justin A. Lemkul, Ph.D. >>>> 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 >>>> >>>> jalemkul@outerbanks.umaryland.****edu <jalemkul@outerbanks.** >>>> umaryland.edu <jalem...@outerbanks.umaryland.edu>> | (410) >>>> 706-7441 >>>> >>>> ==============================****==================== >>>> >>>> >>>> -- >>>> gmx-users mailing list gmx-users@gromacs.org >>>> http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>>> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>>> > >>>> * Please search the archive at http://www.gromacs.org/** >>>> Support/Mailing_Lists/Search<h**ttp://www.gromacs.org/Support/** >>>> Mailing_Lists/Search<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<http://www.gromacs.org/**Support/Mailing_Lists> >>>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>>> > >>>> >>>> >> -- >> ==============================**==================== >> >> Justin A. Lemkul, Ph.D. >> 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 >> >> jalemkul@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu>| >> (410) >> 706-7441 >> >> ==============================**==================== >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> * Please search the archive at http://www.gromacs.org/** >> Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >> > > -- 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
