Re: [AMBER] file contains 2 atoms not in residue templates

From: Jason Swails <>
Date: Tue, 23 Sep 2014 09:46:33 -0400

On Tue, 2014-09-23 at 18:52 +0530, Vishal Nemaysh wrote:
> *Dear all, I am getting a error in leap while loading my .pdb file. How to
> resolve it? the pdb file is also attached herewith. Thanks in advance*
> Created a new atom named: OT1 within residue: .R<CGLU 102>
> Created a new atom named: OT2 within residue: .R<CGLU 102>
> Added missing heavy atom: .R<CGLU 102>.A<O 15>
> Added missing heavy atom: .R<CGLU 102>.A<OXT 16>
> total atoms in file: 838
> Leap added 850 missing atoms according to residue templates:
> 8 Heavy
> 842 H / lone pairs
> The file contained 6 atoms not in residue templates
> > check 1YCC
> Checking '1YCC'....
> WARNING: The unperturbed charge of the unit: 7.000000 is not zero.
> FATAL: Atom .R<ILE 35>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 53>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 74>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 94>.A<CD 20> does not have a type.

The ILE residue does not have an atom named CD. The atom is named CD1.
You have to make sure that the names in the PDB match the names in the
names in the template (the names in the template match the PDB standard
names, so any PDB file you download from the PDB itself should have the
correct atom names for all standard residues already).

Just open your PDB file and modify the names for these ILE residues from
CD to CD1.

> FATAL: Atom .R<CGLU 102>.A<OT1 17> does not have a type.
> FATAL: Atom .R<CGLU 102>.A<OT2 18> does not have a type.

Same with these -- there are 4 carboxylate oxygens in C-terminal
glutamate. The side-chain ones are named OE1 and OE2 and the backbone
ones are named O and OXT.

> Warning: Close contact of 1.420035 angstroms between .R<CALA -1>.A<OXT 11>
> and .R<NGLY 1>.A<CA 5>
> Warning: Close contact of 1.201258 angstroms between .R<CALA -1>.A<OXT 11>
> and .R<NGLY 1>.A<H3 4>
> Warning: Close contact of 0.800222 angstroms between .R<CALA -1>.A<OXT 11>
> and .R<NGLY 1>.A<H2 3>

Wow. You have a lot of bad contacts. You will have to carefully
minimize this to alleviate these steric clashes.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Tue Sep 23 2014 - 07:00:05 PDT
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