Re: [AMBER] problem preparing n-terminus with tleap (?)

From: Matias Machado <>
Date: Wed, 25 Jul 2018 00:07:18 -0300 (UYT)

Dear Julia,

Leap doesn't print the charges in the PDB file (like in a PQR file) so what you are seeing in maestro is due to the way maestro interprets the structure and not the actual parameters used in the AMBER force field (ff14SB). So, parameters are correctly set in the topology (.prmtop file) for the simulation with AMBER... If you have any doubt you can use xleap to visually inspect the atom charges assigned to the structure.

Notice that by default N- and C- terminal residues are treated as zwitterionic, which means Leap will protonate the amine terminal and will generate a carboxy terminal by adding an extra oxygen atom (named OXT, please don't confuse the name with the type). I've never used maestro, but I guess that may be the reason for assigning a formal charge of -1 to OXT...



Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay

----- Mensaje original -----
De: "Julia Belk" <>
Enviados: Martes, 24 de Julio 2018 22:32:26
Asunto: [AMBER] problem preparing n-terminus with tleap (?)

Hi all,

I am not sure if this is a problem or not, but I'm slightly confused --

I am trying to use tleap to prepare some structures, and it seems like
charges are getting assigned differently to the n terminus and the c

After loading and then saving a pdb file, the oxygen at the c terminus is
given type OXT and, when I open the structure in maestro, has a formal
charge of -1. However, the nitrogen at the n terminus is given type N, is
bonded to CH3, but is not given a formal charge of +1.

I don't have much experience with this, but I'm worried that if these
charges aren't assigned correctly it might mess up my simulation, and I
think that that nitrogen should be charged.

Is there a way I can manually fix this? Or is it not a problem?


PS - here is an example of the exact commands I'm running:

1. download pdb file (e.g., 3QDJ (look at the peptide -- chain C))
2. open tleap and run

> source leaprc.protein.ff14SB

> source leaprc.water.tip3p

> mol = loadpdb 3QDJ.pdb

> savepdb mol 3qdj_out.pdb

3. open 3qdj_out.pdb in maestro and inspect peptide termini
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Received on Tue Jul 24 2018 - 20:30:03 PDT
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