Hi Justin, I merge two molecules as a single molecule type. Now I'm trying to do energy minimization of the system, getting errors like
Fatal error: [file topol.top, line 55130]: No default Proper Dih. types Any idea for this type of errors. Thanks --Rama On Mon, Sep 9, 2013 at 1:57 PM, Rama Krishna Koppisetti < ramkishn...@gmail.com> wrote: > 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? 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