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
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