[gmx-users] Incorrect .top file numbering

[Ashutosh Jogalekar]

I am trying to do an MD on a peptide with an unnatural amino acid  
residue. When I convert the pdb to the gro file and generate the .top  
file, the amino acid residues are numbered incorrectly. The first  
three are numbered ok from 1-3. But after the third one, the next one  
is numbered 5 instead of 4, and after that, all the others are  
numbered successively. Why is this happening?
Thanks
Ashutosh Jogalekar
Emory University