<DIV>Hi, people!<BR><BR>I´m doing the simulation in vacuo, then I have no<BR>ions.<BR>Below I send the md.mdp file.<BR>The Index file has Protein_A, Protein_B, MKC and<BR>all residues seen in the md.mdp file.<BR>I want to find the lennard-jones and coulomb<BR>interactions between the ligand MKC and the<BR>residues shown below.<BR>When I run grompp, gromacs return an error, it<BR>says "there is 56 groups, but only 22 tau_t and<BR>ref_t values". But I have put all values! Are<BR>there some limitations in the number of tc_grps<BR>groups?<BR>Thanks,<BR>Monique Brito<BR><BR>md.mdp<BR><BR>title = 1rt1<BR>include =<BR>define
=<BR>integrator = md<BR>dt = 0.001 ; 1 fs time<BR>step<BR>nsteps = 1000000 ; 1000 ps<BR>simulation<BR>nstxout = 500<BR>nstvout = 500<BR>nstlog = 500<BR>nstenergy =
50<BR>nstxtcout = 0<BR>energygrps = MKC Protein_A<BR>Protein_B r_94 r_95 r_96 r_97 r_98 r_99 r_100<BR>r_101 r_102 r_103 r_104 r_105 r_106 r_107 r_108<BR>r_178 r_179 r_180 r_181 r_182 r_183 r_186 r_187<BR>r_188 r_189 r_190 r_191 r_192 r_198 r_223 r_224<BR>r_225 r_226 r_227 r_228 r_229 r_230 r_232 r_233<BR>r_234 r_235 r_236 r_237 r_238 r_239 r_240 r_317<BR>r_318 r_319 r_136 r_137 r_138 r_139<BR>nstlist = 10 ; default value<BR>ns_type = grid<BR>rlist =
0.8<BR>pbc = xyz<BR>coulombtype = PME<BR>pme_order = 4<BR>optimize_fft = yes<BR>rcoulomb = 1.0<BR>rvdw = 0.8<BR>xtc_grps = MKC Protein_A<BR>Protein_B r_94 r_95 r_96 r_97 r_98 r_99 r_100<BR>r_101 r_102 r_103 r_104 r_105 r_106 r_107 r_108<BR>r_178 r_179 r_180 r_181 r_182 r_183 r_186 r_187<BR>r_188 r_189 r_190 r_191
r_192 r_198 r_223 r_224<BR>r_225 r_226 r_227 r_228 r_229 r_230 r_232 r_233<BR>r_234 r_235 r_236 r_237 r_238 r_239 r_240 r_317<BR>r_318 r_319 r_136 r_137 r_138 r_139<BR>tcoupl = Berendsen<BR>tc-grps = MKC Protein_A<BR>Protein_B r_94 r_95 r_96 r_97 r_98 r_99 r_100<BR>r_101 r_102 r_103 r_104 r_105 r_106 r_107 r_108<BR>r_178 r_179 r_180 r_181 r_182 r_183 r_186 r_187<BR>r_188 r_189 r_190 r_191 r_192 r_198 r_223 r_224<BR>r_225 r_226 r_227 r_228 r_229 r_230 r_232 r_233<BR>r_234 r_235 r_236 r_237 r_238 r_239 r_240 r_317<BR>r_318 r_319 r_136 r_137 r_138 r_139<BR>tau_t = 0.1 0.1 0.1 <BR> 0.1 0.1
0.1 0.1 0.1 0.1 0.1 0.1 0.1 <BR>0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 <BR>0.1 0.1<BR>0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 <BR>0.1 0.1 0.1 0.1 0.1<BR>0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 <BR>0.1 0.1 0.1 0.1 0.1<BR>0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1<BR>ref_t = 300 300 300 <BR> 300 300 300 300 300
300 300 300 300 <BR>300 300 300 300 300 300 300 300 <BR>300 300<BR>300 300 300 300 300 300 300 300 <BR>300 300 300 300 300<BR>300 300 300 300 300 300 300 300 <BR>300 300 300 300 300<BR>300 300 300 300 300 300 300 300<BR>Pcoupl = Berendsen<BR>tau_p =
1.0<BR>compressibility = 4.5e-5<BR>ref_p = 1.0<BR>gen_vel = yes<BR>gen_temp = 300<BR>gen_seed = 173529<BR>constraints = none</DIV><p>
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