gmxcheck of my index file gives: Contents of index file index.ndx -------------------------------------------------- Nr. Group #Entries First Last 0 System 2230 1 2230 1 Protein 2226 1 2226 2 Protein-H 2226 1 2226 3 C-alpha 308 3 2218 4 Backbone 922 1 2219 5 MainChain 1232 1 2226 6 MainChain+Cb 1488 1 2226 7 MainChain+H 1232 1 2226 8 SideChain 994 8 2225 9 SideChain-H 994 8 2225 10 Prot-Masses 2226 1 2226 11 non-Protein 4 2227 2230 12 Ion 4 2227 2230 13 CU 2 2227 2229 14 ZN 2 2228 2230 15 r_131_&_chA 8 956 963 16 r_131_&_chB 8 2069 2076 17 r_132 11 1207 1217 18 r_286 11 2611 2621 19 CA_chA_r131 1 1209 1209 20 CA_chB_r131 1 2613 2613
and following are the contents of my .mdp file: title = Umbrella pulling simulation define = -DPOSRES_CA_chA_r131 ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 250000 ; 500 ps nstcomm = 10 ; Output parameters nstxout = 5000 ; every 10 ps nstvout = 5000 nstfout = 500 nstxtcout = 500 ; every 1 ps nstenergy = 500 ; Bond parameters constraint_algorithm = lincs constraints = all-bonds continuation = yes ; continuing from NPT ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb = 1.4 rvdw = 1.4 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in two groups Tcoupl = Nose-Hoover tc_grps = Protein Non-Protein tau_t = 0.5 0.5 ref_t = 310 310 ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = com ; Generate velocities is off gen_vel = no ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr = EnerPres ; Pull code pull = umbrella pull_geometry = distance ; simple distance increase pull_dim = Y N N pull_start = yes ; define initial COM distance > 0 pull_ngroups = 1 pull_group0 = CA_chA_r131 pull_group1 = CA_chB_r131 pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 4200 ; kJ mol^-1 nm^-2 Thanks in advance. Nidhi On Wed, Aug 6, 2014 at 8:06 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 8/6/14, 3:46 AM, Nidhi Katyal wrote: > >> Hello all, >> >> I am working on protein with two chains. I would like to restrain one atom >> of one chain while doing steered MD. For the same reason, I have created >> an >> index file that includes that atom, then created its posre.itp file and >> finally included following lines at the end of topol_Protein_chainA.itp: >> >> ; Include Position restraint file >> #ifdef POSRES_CA_chA_r131 >> #include "posre.itp" >> #endif >> >> I am also pasting a small section of my topol.top file: >> >> >> ; Include forcefield parameters >> #include "gromos53a6.ff/forcefield.itp" >> >> ; Include chain topologies >> #include "topol_Protein_chain_A.itp" >> #include "topol_Protein_chain_B.itp" >> #include "topol_Ion_chain_A2.itp" >> #include "topol_Ion_chain_B2.itp" >> >> ; Include water topology >> #include "gromos53a6.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 >> >> After carrying out NPT equilibration, when I run following command: >> >> grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt >> -o pull.tpr >> >> as given in tutorial: >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ >> gmx-tutorials/umbrella/05_pull.html >> >> I am getting following error: >> 215400 atoms are not part of any of the T-Coupling groups >> >> Since my pull.mdp file as the same as given in tutorial, my coupling >> groups are Protein and Non-Protein. >> I suspect there is something wrong while adding restraints using >> include file mechanism. Please help me resolve the problem. >> >> > The error is not a result of the #include mechanism; it's a problem in the > group definitions, either in the .mdp file or in the index file. Without > the full text of the .mdp and the gmxcheck output of the index.ndx file, > there's little to suggest. > > -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.