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 happens?
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 -- Maria G. Technical University of Denmark Copenhagen
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