[gmx-users] Incorrect .top file numbering
Mark.Abraham at anu.edu.au
Mon Mar 6 20:37:57 CET 2006
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?
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