On Thu, Aug 23, 2012 at 2:32 AM, gargi borgohai <gargib2011.gmail.com>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
residue.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Aug 23 2012 - 08:00:04 PDT
