Re: [AMBER] topology problems

From: Matias Machado <>
Date: Tue, 07 Apr 2020 16:28:09 -0300 (UYT)

Dear Steve,

I'm not truly understanding your issue... leap parse the PDB structure according to the chain IDs and/or TER statements... if you want to have a single/unique continuous polypeptidic chain then name it the same (e.g. "A"), otherwise leap will split it in two (no peptidic bond between A and B is generated) and terminal residues are set accordingly (probably file "leap.log" says "Mapped residue XXX, term: Terminal/beginning...", that is the reason for the introduction of OXT atoms... because by default N and C termini are patch to be zwitterionic (OXT belongs to carboxyl at Ct).


Matias Machado

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

----- Mensaje original -----
De: "Steve Allan Seibold" <>
Enviados: Martes, 7 de Abril 2020 13:58:59
Asunto: [AMBER] topology problems

I have added a protein subunit (called A) to another protein(B) and created one polypeptide chain AB. There are no "TER" commands and the system is recognized and the prmtop and inpcrd files are built using tleap with no problem. The output pdb files (using leap) are fine-one polypeptide chain AB. When I use the output file prmtop to produce a pdb file of the inpcrd file, again there is no problem. It's a AB polypeptide.

However, when I do an energy minimization and convert file.rst to a file.pdb using "ambpdb -p prmtop -c file.rst > file.pdb", the resulting pdb file separates the subunit A from B by creating an "OXT" at the end of A. That is A-oxt and thus becomes a separate subunit. Since the prmtop file does not call for a OXT at that position, how is ambpdb creating it?

I am visualizing using VMD. I even loaded first the prmtop file and then the pdb file (of the restart file) and got A-oxt..

Thanks, Steve
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Received on Tue Apr 07 2020 - 12:30:02 PDT
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