[gmx-users] problem regarding freezegrps

[Erik Marklund]

Try spaces between the brackets and the index labels, e.g. "[ protein ]"

/Erik

14 jul 2007 kl. 07.00 skrev 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
>
>
>
>
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before  
> posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

_______________________________________________
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,	75124 Uppsala, Sweden
phone:	+46 18 471 4537		fax: +46 18 511 755
erikm at xray.bmc.uu.se	http://xray.bmc.uu.se/molbiophys


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20070724/c6fd76b4/attachment.html>