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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