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

From: Julia Belk <jbelk.stanford.edu>
Date: Tue, 24 Jul 2018 18:32:26 -0700

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 - 19:00:02 PDT
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