[gmx-users] terminal proline and OPLSAA charges

Huafeng Xu huafeng at maxwell.compbio.ucsf.edu
Mon Jan 26 20:08:01 CET 2004

I am trying to set up a topology file from a pdb file using pdb2gmx. My
peptide starts with a proline in the N-terminus. I ran the command 
pdb2gmx -f ligand.pdb -o ligand -p ligand -i ligand
chose OPLS-AA/L force field, and noticed that the total charge of the
system, as reported in the output of command, was 1.870e, NOT AN
INTEGER. If I delete the prolines from the N-terminus, the problem goes
away. As long as the peptide starts with a proline at the N-terminus,
the total charge is not an integer. What is going on?  
I am attaching the PDB file of the peptide for your reference.
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