[gmx-users] Grompp error!!!

[Monique Brito]

Hi, people!

I´m doing the simulation in vacuo, then I have no
ions.
Below I send the md.mdp file.
The Index file has Protein_A, Protein_B, MKC and
all  residues seen in the md.mdp file.
I want to find the lennard-jones and coulomb
interactions between the ligand MKC and the
residues shown below.
When I run grompp, gromacs return an error, it
says "there is 56 groups, but only 22 tau_t and
ref_t values". But I have put all values! Are
there some limitations in the number of tc_grps
groups?
Thanks,
Monique Brito

md.mdp

title                    = 1rt1
include                  =
define                   =
integrator               = md
dt                       = 0.001   ; 1 fs time
step
nsteps                   = 1000000 ; 1000 ps
simulation
nstxout                  = 500
nstvout                  = 500
nstlog                   = 500
nstenergy                = 50
nstxtcout                = 0
energygrps               = MKC Protein_A
Protein_B r_94 r_95 r_96 r_97 r_98 r_99 r_100
r_101 r_102 r_103 r_104 r_105 r_106 r_107 r_108
r_178 r_179 r_180 r_181 r_182 r_183 r_186 r_187
r_188 r_189 r_190 r_191 r_192 r_198 r_223 r_224
r_225 r_226 r_227 r_228 r_229 r_230 r_232 r_233
r_234 r_235 r_236 r_237 r_238 r_239 r_240 r_317
r_318 r_319 r_136 r_137 r_138 r_139
nstlist                  = 10  ; default value
ns_type                  = grid
rlist                    = 0.8
pbc                      = xyz
coulombtype              = PME
pme_order                = 4
optimize_fft             = yes
rcoulomb                 = 1.0
rvdw                     = 0.8
xtc_grps                 = MKC Protein_A
Protein_B r_94 r_95 r_96 r_97 r_98 r_99 r_100
r_101 r_102 r_103 r_104 r_105 r_106 r_107 r_108
r_178 r_179 r_180 r_181 r_182 r_183 r_186 r_187
r_188 r_189 r_190 r_191 r_192 r_198 r_223 r_224
r_225 r_226 r_227 r_228 r_229 r_230 r_232 r_233
r_234 r_235 r_236 r_237 r_238 r_239 r_240 r_317
r_318 r_319 r_136 r_137 r_138 r_139
tcoupl                   = Berendsen
tc-grps                  = MKC Protein_A
Protein_B r_94 r_95 r_96 r_97 r_98 r_99 r_100
r_101 r_102 r_103 r_104 r_105 r_106 r_107 r_108
r_178 r_179 r_180 r_181 r_182 r_183 r_186 r_187
r_188 r_189 r_190 r_191 r_192 r_198 r_223 r_224
r_225 r_226 r_227 r_228 r_229 r_230 r_232 r_233
r_234 r_235 r_236 r_237 r_238 r_239 r_240 r_317
r_318 r_319 r_136 r_137 r_138 r_139
tau_t                    = 0.1 0.1       0.1     
 0.1  0.1  0.1  0.1  0.1  0.1  0.1   0.1   0.1  
0.1   0.1   0.1   0.1   0.1   0.1   0.1   0.1  
0.1   0.1
0.1   0.1   0.1   0.1   0.1   0.1   0.1   0.1  
0.1   0.1   0.1   0.1   0.1
0.1   0.1   0.1   0.1   0.1   0.1   0.1   0.1  
0.1   0.1   0.1   0.1   0.1
0.1   0.1   0.1   0.1   0.1   0.1   0.1   0.1
ref_t                    = 300 300       300     
 300  300  300  300  300  300  300   300   300  
300   300   300   300   300   300   300   300  
300   300
300   300   300   300   300   300   300   300  
300   300   300   300   300
300   300   300   300   300   300   300   300  
300   300   300   300   300
300   300   300   300   300   300   300   300
Pcoupl                   = Berendsen
tau_p                    = 1.0
compressibility          = 4.5e-5
ref_p                    = 1.0
gen_vel                  = yes
gen_temp                 = 300
gen_seed                 = 173529
constraints              = none



	
	
		
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