[gmx-users] VAL group

[Owen, Michael]

Hello  fellow gmx users,

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.

An excert from the topology file that shows the structure contains one peptide is below.

[ system ]
; Name
Protein in water

[ molecules ]
; Compound        #mols
Protein             1
SOL              6973

An excerpt from the index file that shows the VAL group containing 16 atoms is below. 


28125 28126 28127 28128 28129 28130 28131 28132 28133 28134 28135 28136 28137 28138 28139 
28140 28141 28142 28143 28144 28145 28146 28147 28148 28149 28150 28151 28152 28153 28154 
28155 28156 28157 28158 28159 28160 28161 28162 
[ VAL ]
 154  155  156  157  158  159  160  161  162  163  164  165  166  167  168 
 169 
[ SOL ]
 271  272  273  274  275  276  277  278  279  280  281  282  283  284  285 
 286  287  288  289  290  291  292  293  294  295  296  297  298  299  300 
 301  302  303  304  305  306  307  308  309  310  311  312  313  314  315 


Could something be wrong with the pdb2gmx program?

Thank you in advance for any suggestions.

Sincerely,

Michael Owen
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