Hello sir,<br><br>Thanks for such a explanatory tutorial.<br>I am stuck with one error now.<br>I have protein, popc, sol and cl- in my system.<br>I have merged the sol and cl- using make_ndx.<br>But when I run grompp I get the error like this "popc not defined in the index file".<br>
The grompp command : grompp -f pr.mdp -c box_em.pdb -p topol.top -o box_pr.tpr<br>Any suggestions please.<br><b><br>pr.mdp file :</b><br>title = protein in popc bilayer<br>cpp = /usr/bin/cpp<br>
define = -DPOSRES -DPOSRES_LIPID<br>constraints = all-bonds<br>constraint-algorithm= Lincs<br>integrator = md<br>dt = 0.002 <br>nsteps = 5000 <br>nstcomm = 1<br>
nstxout = 50<br>nstvout = 1000<br>nstfout = 0<br>nstlog = 10<br>nstenergy = 10<br>nstlist = 10<br>ns_type = grid<br>rlist = 1<br>
coulombtype = PME<br>rcoulomb = 1<br>vdw-type = Cut-off<br>rvdw = 1<br>; Berendsen temperature coupling is on in two groups<br>tcoupl = berendsen<br>tc_grps = Protein POPC SOL_CL-<br>
tau_t = 0.1 0.1 0.1 <br>ref_t = 300 300 300<br>; Energy monitoring<br>energygrps = Protein POPC SOL_CL-<br>; Pressure coupling is on<br>;Pcoupl = berendsen<br>tau_p = 2.0 2.0<br>
compressibility = 4.5e-5 4.5e-5<br>ref_p = 1.0 1.0<br>Pcoupl_type = semiisotropic<br>; Generate velocites is on at 300 K.<br>gen_vel = yes<br>gen_temp = 300.0<br>gen_seed = 173529<br>
<br>Thanking you,<br>Pawan<br>