[gmx-users] terminal proline and OPLSAA charges

Marc Ceruso mceruso at physbio.mssm.edu
Mon Jan 26 20:12:01 CET 2004

Messagemake sure you use the N-term pro option in pdbgmx and check atom
types for N-term patch in .top and .rtp (library file)
  -----Original Message-----
  From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]On
Behalf Of Huafeng Xu
  Sent: Monday, January 26, 2004 2:07 PM
  To: gmx-users at gromacs.org
  Subject: [gmx-users] terminal proline and OPLSAA charges

  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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