[gmx-users] Incorrect .top file numbering

Ashutosh Jogalekar ajogale at emory.edu
Mon Mar 6 18:17:35 CET 2006

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?
Ashutosh Jogalekar
Emory University

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