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)
-- residue 55: duplicate [ CG] atoms (total 2)
-- residue 55: duplicate [ CZ] atoms (total 2)
-- residue 55: duplicate [ HB2] atoms (total 2)
-- residue 55: duplicate [ HB3] atoms (total 2)
-- residue 55: duplicate [ HD2] atoms (total 2)
-- residue 55: duplicate [ HD3] atoms (total 2)
-- residue 55: duplicate [ HE] atoms (total 2)
-- residue 55: duplicate [ HG2] atoms (total 2)
-- residue 55: duplicate [ HG3] atoms (total 2)
-- residue 55: duplicate [ NE] atoms (total 2)
-- residue 55: duplicate [ NH1] atoms (total 2)
-- residue 55: duplicate [ NH2] atoms (total 2)
-- residue 55: duplicate [HH11] atoms (total 2)
-- residue 55: duplicate [HH12] atoms (total 2)
-- residue 55: duplicate [HH21] atoms (total 2)
-- residue 55: duplicate [HH22] atoms (total 2)
-- residue 56: duplicate [ CB] atoms (total 2)
-- residue 56: duplicate [ HB2] atoms (total 2)
-- residue 56: duplicate [ HB3] atoms (total 2)
-- residue 56: duplicate [ HG] atoms (total 2)
-- residue 56: duplicate [ OG] atoms (total 2)
-- residue 67: duplicate [ CB] atoms (total 2)
-- residue 67: duplicate [ CD] atoms (total 2)
-- residue 67: duplicate [ CG] atoms (total 2)
-- residue 67: duplicate [ NE2] atoms (total 2)
-- residue 67: duplicate [ OE1] atoms (total 2)
-- residue 67: duplicate [HE21] atoms (total 2)
-- residue 67: duplicate [HE22] atoms (total 2)
-- residue 72: duplicate [ CB] atoms (total 2)
-- residue 72: duplicate [ CD] atoms (total 2)
-- residue 72: duplicate [ CG] atoms (total 2)
-- residue 72: duplicate [ HB2] atoms (total 2)
-- residue 72: duplicate [ HB3] atoms (total 2)
-- residue 72: duplicate [ HG2] atoms (total 2)
-- residue 72: duplicate [ HG3] atoms (total 2)
-- residue 72: duplicate [ OE1] atoms (total 2)
-- residue 72: duplicate [ OE2] atoms (total 2)
-- 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.)
Unknown residue: NLE number: 23 type: Nonterminal
Unknown residue: NLE number: 28 type: Nonterminal
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>
Created a new atom named: CA within residue: .R<NLE 65>
Created a new atom named: C within residue: .R<NLE 65>
Created a new atom named: O within residue: .R<NLE 65>
Created a new atom named: CB within residue: .R<NLE 65>
Created a new atom named: CG within residue: .R<NLE 65>
Created a new atom named: CD within residue: .R<NLE 65>
Created a new atom named: CE within residue: .R<NLE 65>
Created a new atom named: H within residue: .R<NLE 65>
Created a new atom named: HA within residue: .R<NLE 65>
Created a new atom named: HB2 within residue: .R<NLE 65>
Created a new atom named: HB3 within residue: .R<NLE 65>
Created a new atom named: HG2 within residue: .R<NLE 65>
Created a new atom named: HG3 within residue: .R<NLE 65>
Created a new atom named: HD2 within residue: .R<NLE 65>
Created a new atom named: HD3 within residue: .R<NLE 65>
Created a new atom named: HE1 within residue: .R<NLE 65>
Created a new atom named: HE2 within residue: .R<NLE 65>
Created a new atom named: HE3 within residue: .R<NLE 65>
One sided connection. Residue: missing connect1 atom.
Created a new atom named: HD1 within residue: .R<HIE 68>
Creating new UNIT for residue: NLE sequence: 70
One sided connection. Residue: missing connect0 atom.
Created a new atom named: N within residue: .R<NLE 70>
Created a new atom named: CA within residue: .R<NLE 70>
Created a new atom named: C within residue: .R<NLE 70>
Created a new atom named: O within residue: .R<NLE 70>
Created a new atom named: CB within residue: .R<NLE 70>
Created a new atom named: CG within residue: .R<NLE 70>
Created a new atom named: CD within residue: .R<NLE 70>
Created a new atom named: CE within residue: .R<NLE 70>
Created a new atom named: H within residue: .R<NLE 70>
Created a new atom named: HA within residue: .R<NLE 70>
Created a new atom named: HB2 within residue: .R<NLE 70>
Created a new atom named: HB3 within residue: .R<NLE 70>
Created a new atom named: HG2 within residue: .R<NLE 70>
Created a new atom named: HG3 within residue: .R<NLE 70>
Created a new atom named: HD2 within residue: .R<NLE 70>
Created a new atom named: HD3 within residue: .R<NLE 70>
Created a new atom named: HE1 within residue: .R<NLE 70>
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.
FATAL: Atom .R<NLE 65>.A<CA 2> does not have a type.
FATAL: Atom .R<NLE 65>.A<C 3> does not have a type.
FATAL: Atom .R<NLE 65>.A<O 4> does not have a type.
FATAL: Atom .R<NLE 65>.A<CB 5> does not have a type.
FATAL: Atom .R<NLE 65>.A<CG 6> does not have a type.
FATAL: Atom .R<NLE 65>.A<CD 7> does not have a type.
FATAL: Atom .R<NLE 65>.A<CE 8> does not have a type.
FATAL: Atom .R<NLE 65>.A<H 9> does not have a type.
FATAL: Atom .R<NLE 65>.A<HA 10> does not have a type.
FATAL: Atom .R<NLE 65>.A<HB2 11> does not have a type.
FATAL: Atom .R<NLE 65>.A<HB3 12> does not have a type.
FATAL: Atom .R<NLE 65>.A<HG2 13> does not have a type.
FATAL: Atom .R<NLE 65>.A<HG3 14> does not have a type.
FATAL: Atom .R<NLE 65>.A<HD2 15> does not have a type.
FATAL: Atom .R<NLE 65>.A<HD3 16> does not have a type.
FATAL: Atom .R<NLE 65>.A<HE1 17> does not have a type.
FATAL: Atom .R<NLE 65>.A<HE2 18> does not have a type.
FATAL: Atom .R<NLE 65>.A<HE3 19> does not have a type.
FATAL: Atom .R<HIE 68>.A<HD1 18> does not have a type.
FATAL: Atom .R<NLE 70>.A<N 1> does not have a type.
FATAL: Atom .R<NLE 70>.A<CA 2> does not have a type.
FATAL: Atom .R<NLE 70>.A<C 3> does not have a type.
FATAL: Atom .R<NLE 70>.A<O 4> does not have a type.
FATAL: Atom .R<NLE 70>.A<CB 5> does not have a type.
FATAL: Atom .R<NLE 70>.A<CG 6> does not have a type.
FATAL: Atom .R<NLE 70>.A<CD 7> does not have a type.
FATAL: Atom .R<NLE 70>.A<CE 8> does not have a type.
FATAL: Atom .R<NLE 70>.A<H 9> does not have a type.
FATAL: Atom .R<NLE 70>.A<HA 10> does not have a type.
FATAL: Atom .R<NLE 70>.A<HB2 11> does not have a type.
FATAL: Atom .R<NLE 70>.A<HB3 12> does not have a type.
FATAL: Atom .R<NLE 70>.A<HG2 13> does not have a type.
FATAL: Atom .R<NLE 70>.A<HG3 14> does not have a type.
FATAL: Atom .R<NLE 70>.A<HD2 15> does not have a type.
FATAL: Atom .R<NLE 70>.A<HD3 16> does not have a type.
FATAL: Atom .R<NLE 70>.A<HE1 17> does not have a type.
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.
>
What should I do to load the protein ? Please help me.
Thanking You.
Sincerely
Gargi Borgohain.
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Received on Thu Aug 23 2012 - 00:00:03 PDT
