Re: [AMBER] loading of a mutant protein in XLEaP

From: Jason Swails <>
Date: Thu, 23 Aug 2012 10:33:55 -0400

On Thu, Aug 23, 2012 at 2:32 AM, gargi borgohai <>wrote:

> Dear Amber users,
> I have downloaded the pdb file of mutant chicken
> villin protein (PDB ID 2F4K) from RCSB protein data bank. But while I tried
> to load the protein in XLEaP (using ff99SB force field) the following lines
> appeared in the terminal window :
> x= loadpdb 2F4K.pdb
> Loading PDB file: ./2F4K.pdb
> -- residue 55: duplicate [ CB] atoms (total 2)
> -- residue 55: duplicate [ CD] atoms (total 2)
> [snip]
> -- residue 109: duplicate [ O] atoms (total 2)
> Warning: Atom names in each residue should be unique.
> (Same-name atoms are handled by using the first
> occurrence and by ignoring the rest.
> Frequently duplicate atom names stem from alternate
> conformations in the PDB file.)

These are fine, and are just warnings. This will happen if your PDB file
has multiple conformations.

Unknown residue: NLE number: 23 type: Nonterminal
> Unknown residue: NLE number: 28 type: Nonterminal

This is a non-standard residue, and is not in any of the Amber residue
libraries. Therefore, you will have to generate (or find) a library for
this residue. I can't tell what it is by that 3-letter code, but the PDB
should have described what that residue is. R.E.D. tools is helpful for
generating library files.

Creating new UNIT for residue: NLE sequence: 65
> One sided connection. Residue: missing connect0 atom.
> Created a new atom named: N within residue: .R<NLE 65>
> [snip]
> Created a new atom named: HE2 within residue: .R<NLE 70>
> Created a new atom named: HE3 within residue: .R<NLE 70>
> One sided connection. Residue: missing connect1 atom.
> total atoms in file: 654
> Leap added 119 missing atoms according to residue templates:
> 119 H / lone pairs
> The file contained 39 atoms not in residue templates
> > saveamberparm x 2f4k.prmtop 2f4k.inpcrd
> Checking Unit.
> FATAL: Atom .R<NLE 65>.A<N 1> does not have a type.
> [snip]
> FATAL: Atom .R<NLE 70>.A<HE2 18> does not have a type.
> FATAL: Atom .R<NLE 70>.A<HE3 19> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.

The above error occurs again because there is no library entry for the NLE


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Thu Aug 23 2012 - 08:00:04 PDT
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