[gmx-users] Incorrect .top file numbering

[Mark Abraham]

Ashutosh Jogalekar wrote:
> 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?

We needed more information. Where is the unnatural amino acid? What does 
your pdb file have in the region 3-5?

Mark