Re: [AMBER] Error creating topology and coordinates file

From: Matias Machado <>
Date: Thu, 12 Sep 2019 11:01:46 -0300 (UYT)

Dear Charalampos,

OXT is expected in C terminal residues, while H2 and H3 are expected in N terminal residues...

My guess is that passing the PDB structure through Desmond either removed the TER statements or the Chain IDs, which in any case prevented AMBER (LEAP) from correctly define ASP and PRO as terminals (CASP, NPRO).

If that was the case, then you should see a (long?) bond linking the backbone atoms of both residues while visualizing the topology and coordinate in VMD (i.e. "vmd TOP.prmtop CORD.rst7")



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

----- Mensaje original -----
Para: "AMBER Mailing List" <>
Enviados: Lunes, 2 de Septiembre 2019 6:58:21
Asunto: Re: [AMBER] Error creating topology and coordinates file

An Update:
Deleting the lines in the pdb containing those atoms and repeating the
process creates the topology and coordinates files normally but I am
not sure if I should do this as I am new to molecular dynamics
My original pdb file is 1RAM.

So my extra question is if it is alright to just delete them?

Thank you,


> Hello everyone,
> I want to perform MM/GBSA and MM/PBSA analysis using trajectories
> created from Desmond. As far as I know, I have to create coordinates
> and topology files for the complex, the ligand (which in my case is
> DNA oligo) and the protein ( which in my case is a Transcription
> Factor).
> My method until now is to take the file-in.cms from Desmond remove the
> waters and the ions and then export the pdb. Then I pass this pdb to
> tleap to export the topology and the coordinates file.
> $ tleap
>> source leaprc.protein.ff14SB
>> source leaprc.DNA.OL15
>> PDB = loadpdb complex.pdb
> Loading PDB file: ./complex.pdb
> Created a new atom named: OXT within residue: .R<ASP 313>
> Created a new atom named: H2 within residue: .R<PRO 314>
> Created a new atom named: H3 within residue: .R<PRO 314>
> total atoms in file: 9906
> The file contained 3 atoms not in residue templates
>> saveamberparm PDB TOP.prmtop CORD.rst7
> At this step the following error occurs:
> Checking Unit.
> Warning: There is a bond of 84.639821 angstroms between:
> Warning: The unperturbed charge of the unit (-36.000000) is not zero.
> FATAL: Atom .R<ASP 313>.A<OXT 13> does not have a type.
> FATAL: Atom .R<PRO 314>.A<H2 15> does not have a type.
> FATAL: Atom .R<PRO 314>.A<H3 16> does not have a type.
> Error: Failed to generate parameters
> Warning: Parameter file was not saved.
> Is there a way to fix it or is there another way to create the
> topology and coordinates files?
> Thank you very much!
> My best regards.
> Charalampos
> _______________________________________________
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Received on Thu Sep 12 2019 - 07:30:02 PDT
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