[gmx-users] problem regarding freezegrps

[gurpreet singh]

Hello Users

i am carrying out a dimeric protein simulation with G43a1 force field using
Gromacs 3.3

I  have added some missing residues into my protein using a seperate
program. Now before adding water i want to do some simulation in vaccum to
minimized those added resideus and also the hydrogens added via pdb2gmx
command.

For these i am freezing the protein and crystal waters leaving the added
residues so that they can freely move. for that i am using the following
input (.mdp)  file:


 title               = minimizatio in vaccum
integrator          = steep
dt                  = 0.002
constraints         = none
nsteps              = 500
nstlist             = 10
rcoulomb            = 1
rvdw                = 1
ns_type             = simple
coulombtype         = PME
vdwtype             = cut-off
pbc                 = no
gen_vel             = no
freezegrps          = protein  solvent
freezedim           = Y Y Y     Y Y Y

emtol               = 100.0
emstep              = 0.01

With that  i have made an index file where i have mentioned two groups with
names 'protein' and 'solvent'

but inspite of this i am getting the following problem :
....................................................

Fatal error:
Group protein not found in indexfile.
Maybe you have non-default goups in your mdp file, while not using the '-n'
option of grompp.
In that case use the '-n' option.
................................................

although i have mentioned the index file in the grompp :

"aquapo.ndx is the name of  index file "
grompp -f 1min.mdp -c aquapo_grom.pdb -p aquapo_grom.top -n aquapo.ndx -o
1min.tpr


index file used
 [protein]
  1 2 3 4 5 6 7 8 9 11 12 13 14 15 16 17 18 19 20 21 22 23 24 26 27 28 29 30
31 32 33 34 35 37 38 39 40 41 42 43 44 45 47 48 49 50 51 52 53 55 56 57 58
59 60  61 64 65 66 67 68 69 70 72 73 74 75 76 77 78 79 80 81 83 85 86 87 88
89 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 110 111
112 113 114   115 116 117 118 119 120 121 122 123 125 126 127 128 129 130
131 132 133 134 136 137 138 139 140 141 142 143 144 146 147 148 149 150 151
152 154 155 156 157  158 159 160 163 164 165 166 167 168 169 171 172 173 174
175 176 177 178 179 180 182 184 185 186 187 188 190 191 192 193 194 195 196
197 198


  [solvent]
  199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216
217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 234 235 236
237 238  239 240 241 242  243 244 245 246 247 248 249 250 251 252 253 254
255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273
274 275



please tell what is the reason for this error

waiting for your reply
With Regards
Gurpreet
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