[AMBER] error in leap prmtop incprd preparation

From: senal dinuka <senal.ichemc.edu.lk>
Date: Sun, 15 Jul 2018 20:40:59 +0530

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 - 08:30:01 PDT
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