[gmx-users] for a single amino acid with NH3+ and COO- terminii, pdb2gmx gives a total charge of -1.1 in OPLSAA ?

maria goranovic mariagoranovic at gmail.com
Tue Jun 1 15:57:29 CEST 2010

I tried pdb2gmx with an alanine pdb file, with options 5 (opls force
field),  0 (NH3+ n-terminus) and 0 (COO- C-terminus). When I run grompp on
the output from pdb2gmx, I get a total charge of -1.1. Any ideas why this

The same problem is not there if one looks at a dipeptide. Why the problem
for a single amino acid? It looks like when pdb2gmx applies patches for the
N-terminus and C-terminus to the ends of a protein, it changes atom types
for the peptide backbone. If one uses a single amino acid, the patches are
applied to the same residue, and hence the odd -1.1 charge? If this is so,
is this not a bug?

Thank you for inputs,


Maria G.
Technical University of Denmark
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