<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><DIV>Try spaces between the brackets and the index labels, e.g. "[ protein ]"</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>/Erik</DIV><BR><DIV><DIV>14 jul 2007 kl. 07.00 skrev gurpreet singh:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite">Hello Users<BR> <BR> i am carrying out a dimeric protein simulation with G43a1 force field using Gromacs 3.3<BR> <BR> 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.<BR> <BR> 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:<BR> <BR> <BR> title = minimizatio in vaccum<BR> integrator = steep<BR> dt = 0.002<BR> constraints = none<BR> nsteps = 500<BR> nstlist = 10<BR> rcoulomb = 1<BR> rvdw = 1<BR> ns_type = simple<BR> coulombtype = PME<BR> vdwtype = cut-off<BR> pbc = no<BR> gen_vel = no<BR> freezegrps = protein solvent<BR> freezedim = Y Y Y Y Y Y<BR> <BR> emtol = 100.0<BR> emstep = 0.01<BR> <BR> With that i have made an index file where i have mentioned two groups with names 'protein' and 'solvent' <BR> <BR> but inspite of this i am getting the following problem :<BR> ....................................................<BR> <BR> Fatal error:<BR> Group protein not found in indexfile.<BR> Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp.<BR> In that case use the '-n' option.<BR> ................................................<BR> <BR> although i have mentioned the index file in the grompp :<BR> <BR> "aquapo.ndx is the name of index file "<BR> grompp -f 1min.mdp -c aquapo_grom.pdb -p aquapo_grom.top -n aquapo.ndx -o 1min.tpr <BR> <BR> <BR> index file used <BR> [protein]<BR> 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<BR> <BR> <BR> [solvent]<BR> 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<BR> <BR> <BR> <BR> please tell what is the reason for this error <BR> <BR> waiting for your reply <BR> With Regards<BR> Gurpreet<BR> <BR> <BR> <BR> <BR> <BR><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">gmx-users mailing list<SPAN class="Apple-converted-space"> </SPAN><A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Please search the archive at <A href="http://www.gromacs.org/search">http://www.gromacs.org/search</A> before posting!</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Please don't post (un)subscribe requests to the list. Use the<SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">www interface or send it to <A href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Can't post? Read <A href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</A></DIV> </BLOCKQUOTE></DIV><BR><DIV> <SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><BLOCKQUOTE type="cite"></BLOCKQUOTE><DIV>_______________________________________________</DIV><DIV>Erik Marklund, PhD student</DIV><DIV>Laboratory of Molecular Biophysics,</DIV><DIV>Dept. of Cell and Molecular Biology, Uppsala University.</DIV><DIV>Husargatan 3, Box 596,<SPAN class="Apple-tab-span" style="white-space:pre"><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "> </SPAN></SPAN></SPAN></SPAN>75124 Uppsala, Sweden</DIV><DIV>phone:<SPAN class="Apple-tab-span" style="white-space:pre"><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "> </SPAN></SPAN></SPAN></SPAN>+46 18 471 4537<SPAN class="Apple-tab-span" style="white-space:pre"><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "> </SPAN></SPAN></SPAN></SPAN>fax: +46 18 511 755</DIV><DIV><A href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</A><SPAN class="Apple-tab-span" style="white-space:pre"><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "> </SPAN></SPAN></SPAN></SPAN>http://xray.bmc.uu.se/molbiophys</DIV><BR class="Apple-interchange-newline"></SPAN></SPAN></SPAN></SPAN> </DIV><BR></BODY></HTML>