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<P><FONT SIZE=2>Hello fellow gmx users,<BR>
<BR>
when I convert a pdb file of a peptide that contains a valyl residue into a .gro file a separate "group" is made for the atoms in the valyl residue. This has happened when OPLSAA/l and the GROMOS96 53a6 force fields were used. The molecule appears as one in the topology file, and the atomic description of the valyl residue in the pdb file matches that of the ffoplsa.rtp file.<BR>
<BR>
An excert from the topology file that shows the structure contains one peptide is below.<BR>
<BR>
[ system ]<BR>
; Name<BR>
Protein in water<BR>
<BR>
[ molecules ]<BR>
; Compound #mols<BR>
Protein 1<BR>
SOL 6973<BR>
<BR>
An excerpt from the index file that shows the VAL group containing 16 atoms is below.<BR>
<BR>
<BR>
28125 28126 28127 28128 28129 28130 28131 28132 28133 28134 28135 28136 28137 28138 28139<BR>
28140 28141 28142 28143 28144 28145 28146 28147 28148 28149 28150 28151 28152 28153 28154<BR>
28155 28156 28157 28158 28159 28160 28161 28162<BR>
[ VAL ]<BR>
154 155 156 157 158 159 160 161 162 163 164 165 166 167 168<BR>
169<BR>
[ SOL ]<BR>
271 272 273 274 275 276 277 278 279 280 281 282 283 284 285<BR>
286 287 288 289 290 291 292 293 294 295 296 297 298 299 300<BR>
301 302 303 304 305 306 307 308 309 310 311 312 313 314 315<BR>
<BR>
<BR>
Could something be wrong with the pdb2gmx program?<BR>
<BR>
Thank you in advance for any suggestions.<BR>
<BR>
Sincerely,<BR>
<BR>
Michael Owen<BR>
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