Re: [AMBER] error in leap prmtop incprd preparation

From: Matias Machado <>
Date: Sun, 15 Jul 2018 19:59:11 -0300 (UYT)

Dear Senal,

Leap can add hydrogens (and other missing atoms) to the structure, so in principle you don't need protonated structures just the correct residue names to describe the desired protonation state which is important in case of HIS, GLU, ASP and LYS residues.

Notice that, HE2 and HD2 are common hydrogen names describing protonated GLU and ASP residues (GLH and ASH in AMBER). Those hydrogens may be added when pH is considered in the algorithms for protonation. I generally use pdb2pqr to set the protonation according to a pH and I choose the naming scheme of AMBER so the affected residues are renamed accordingly. I've never used H++, but it may not change the residue names despite adding the protons. That is important, because other force fields (e.g. CHARMM or GROMOS) use the same residue name to refer acidic or protonated states.

So to solve this issue you have to edit the PDB file to either delete those hydrogens from GLU 277 and ASP 391 in case you want to simulate negative charged (acidic) residues or you have to rename GLU(277) and ASP(391) to GLH and ASH to describe the neutral states.



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

----- Mensaje original -----
De: "senal dinuka" <>
Para: "AMBER Mailing List" <>
Enviados: Domingo, 15 de Julio 2018 12:10:59
Asunto: [AMBER] error in leap prmtop incprd preparation

Dear Amber uses,

I have been trying to generate prmtop and inpcrd files for pdb id 1eve
protonated using H++ server and standardized through pdb4amber. When using
tleap it creates two new H atom under two residues which seems to cause the
error. I didn't use reduce in amber which then would changes protonation
states in my pdb file. On using original pdb file from the database
standardized using pdb4amber also results in the same error.

Loading PDB file: ./ache-amber.pdb
Created a new atom named: HE2 within residue: .R<GLU 277>
Created a new atom named: HD2 within residue: .R<ASP 391>
  total atoms in file: 8386
  The file contained 2 atoms not in residue templates
Checking 'ache'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
FATAL: Atom .R<GLU 277>.A<HE2 16> does not have a type.
FATAL: Atom .R<ASP 391>.A<HD2 13> does not have a type.
Warning: Close contact of 0.961525 angstroms between .R<GLU 277>.A<OE2 13>
and .R<GLU 277>.A<HE2 16>
Warning: Close contact of 0.960572 angstroms between .R<ASP 391>.A<OD2 10>
and .R<ASP 391>.A<HD2 13>
Checking parameters for unit 'ache'.
Checking for bond parameters.
Checking for angle parameters.
check: Errors: 2 Warnings: 3

What could be the reason and possible solution?

D L Senal Dinuka
Grad.Chem., A.I.Chem.C.
Research Assistant
College of Chemical Sciences
Institute of Chemistry Ceylon
Sri Lanka
+94 77 627 4678
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Received on Sun Jul 15 2018 - 16:30:01 PDT
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