AMBER Archive (2009)

Subject: Re: [AMBER] Output Does Not Match in Tutorial B1

From: Wallace Kunin (kunin_at_marshall.edu)
Date: Mon Nov 30 2009 - 13:11:02 CST

I used tleap and left out the quotation marks. Here is the output:

> model = loadpdb nuc_ter.pdb
> Loading PDB file: ./nuc_ter.pdb
> Unknown residue: A5 number: 0 type: Terminal/beginning
> ..relaxing end constraints to try for a dbase match
> -no luck
> Unknown residue: A3 number: 9 type: Terminal/last
> ..relaxing end constraints to try for a dbase match
> -no luck
> Unknown residue: T5 number: 10 type: Terminal/beginning
> ..relaxing end constraints to try for a dbase match
> -no luck
> Unknown residue: T number: 11 type: Nonterminal
> Unknown residue: T number: 12 type: Nonterminal
> Unknown residue: T number: 13 type: Nonterminal
> Unknown residue: T number: 14 type: Nonterminal
> Unknown residue: T number: 15 type: Nonterminal
> Unknown residue: T number: 16 type: Nonterminal
> Unknown residue: T number: 17 type: Nonterminal
> Unknown residue: T number: 18 type: Nonterminal
> Unknown residue: T3 number: 19 type: Terminal/last
> ..relaxing end constraints to try for a dbase match
> -no luck
> Creating new UNIT for residue: A5 sequence: 1
> Created a new atom named: H5T within residue: .R<A5 1>
> Created a new atom named: O3' within residue: .R<A5 1>
> Created a new atom named: O5' within residue: .R<A5 1>
> Created a new atom named: C1' within residue: .R<A5 1>
> Created a new atom named: C2' within residue: .R<A5 1>
> Created a new atom named: C3' within residue: .R<A5 1>
> Created a new atom named: C4' within residue: .R<A5 1>
> Created a new atom named: C5' within residue: .R<A5 1>
> Created a new atom named: O4' within residue: .R<A5 1>
> Created a new atom named: N6 within residue: .R<A5 1>
> Created a new atom named: H61 within residue: .R<A5 1>
> Created a new atom named: H62 within residue: .R<A5 1>
> Created a new atom named: C6 within residue: .R<A5 1>
> Created a new atom named: C5 within residue: .R<A5 1>
> Created a new atom named: N7 within residue: .R<A5 1>
> Created a new atom named: C8 within residue: .R<A5 1>
> Created a new atom named: N9 within residue: .R<A5 1>
> Created a new atom named: C4 within residue: .R<A5 1>
> Created a new atom named: N3 within residue: .R<A5 1>
> Created a new atom named: C2 within residue: .R<A5 1>
> Created a new atom named: N1 within residue: .R<A5 1>
> One sided connection. Residue: missing connect1 atom.
> Added missing heavy atom: .R<RA 2>.A<O2' 31>
> Added missing heavy atom: .R<RA 3>.A<O2' 31>
> Added missing heavy atom: .R<RA 4>.A<O2' 31>
> Added missing heavy atom: .R<RA 5>.A<O2' 31>
> Added missing heavy atom: .R<RA 6>.A<O2' 31>
> Added missing heavy atom: .R<RA 7>.A<O2' 31>
> Added missing heavy atom: .R<RA 8>.A<O2' 31>
> Added missing heavy atom: .R<RA 9>.A<O2' 31>
> Creating new UNIT for residue: A3 sequence: 10
> One sided connection. Residue: missing connect0 atom.
> Created a new atom named: P within residue: .R<A3 10>
> Created a new atom named: O1P within residue: .R<A3 10>
> Created a new atom named: O2P within residue: .R<A3 10>
> Created a new atom named: O3' within residue: .R<A3 10>
> Created a new atom named: O5' within residue: .R<A3 10>
> Created a new atom named: C1' within residue: .R<A3 10>
> Created a new atom named: C2' within residue: .R<A3 10>
> Created a new atom named: C3' within residue: .R<A3 10>
> Created a new atom named: C4' within residue: .R<A3 10>
> Created a new atom named: C5' within residue: .R<A3 10>
> Created a new atom named: O4' within residue: .R<A3 10>
> Created a new atom named: N6 within residue: .R<A3 10>
> Created a new atom named: H61 within residue: .R<A3 10>
> Created a new atom named: H62 within residue: .R<A3 10>
> Created a new atom named: C6 within residue: .R<A3 10>
> Created a new atom named: C5 within residue: .R<A3 10>
> Created a new atom named: N7 within residue: .R<A3 10>
> Created a new atom named: C8 within residue: .R<A3 10>
> Created a new atom named: N9 within residue: .R<A3 10>
> Created a new atom named: C4 within residue: .R<A3 10>
> Created a new atom named: N3 within residue: .R<A3 10>
> Created a new atom named: C2 within residue: .R<A3 10>
> Created a new atom named: N1 within residue: .R<A3 10>
> Created a new atom named: H3T within residue: .R<A3 10>
> Creating new UNIT for residue: T5 sequence: 11
> Created a new atom named: H5T within residue: .R<T5 11>
> Created a new atom named: O3' within residue: .R<T5 11>
> Created a new atom named: O5' within residue: .R<T5 11>
> Created a new atom named: C1' within residue: .R<T5 11>
> Created a new atom named: C2' within residue: .R<T5 11>
> Created a new atom named: C3' within residue: .R<T5 11>
> Created a new atom named: C4' within residue: .R<T5 11>
> Created a new atom named: C5' within residue: .R<T5 11>
> Created a new atom named: O4' within residue: .R<T5 11>
> Created a new atom named: O4 within residue: .R<T5 11>
> Created a new atom named: C4 within residue: .R<T5 11>
> Created a new atom named: N3 within residue: .R<T5 11>
> Created a new atom named: H3 within residue: .R<T5 11>
> Created a new atom named: C2 within residue: .R<T5 11>
> Created a new atom named: O2 within residue: .R<T5 11>
> Created a new atom named: N1 within residue: .R<T5 11>
> Created a new atom named: C6 within residue: .R<T5 11>
> Created a new atom named: C5 within residue: .R<T5 11>
> Created a new atom named: C7 within residue: .R<T5 11>
> Creating new UNIT for residue: T sequence: 12
> Created a new atom named: P within residue: .R<T 12>
> Created a new atom named: O1P within residue: .R<T 12>
> Created a new atom named: O2P within residue: .R<T 12>
> Created a new atom named: O3' within residue: .R<T 12>
> Created a new atom named: O5' within residue: .R<T 12>
> Created a new atom named: C1' within residue: .R<T 12>
> Created a new atom named: C2' within residue: .R<T 12>
> Created a new atom named: C3' within residue: .R<T 12>
> Created a new atom named: C4' within residue: .R<T 12>
> Created a new atom named: C5' within residue: .R<T 12>
> Created a new atom named: O4' within residue: .R<T 12>
> Created a new atom named: O4 within residue: .R<T 12>
> Created a new atom named: C4 within residue: .R<T 12>
> Created a new atom named: N3 within residue: .R<T 12>
> Created a new atom named: H3 within residue: .R<T 12>
> Created a new atom named: C2 within residue: .R<T 12>
> Created a new atom named: O2 within residue: .R<T 12>
> Created a new atom named: N1 within residue: .R<T 12>
> Created a new atom named: C6 within residue: .R<T 12>
> Created a new atom named: C5 within residue: .R<T 12>
> Created a new atom named: C7 within residue: .R<T 12>
> Creating new UNIT for residue: T sequence: 13
> Created a new atom named: P within residue: .R<T 13>
> Created a new atom named: O1P within residue: .R<T 13>
> Created a new atom named: O2P within residue: .R<T 13>
> Created a new atom named: O3' within residue: .R<T 13>
> Created a new atom named: O5' within residue: .R<T 13>
> Created a new atom named: C1' within residue: .R<T 13>
> Created a new atom named: C2' within residue: .R<T 13>
> Created a new atom named: C3' within residue: .R<T 13>
> Created a new atom named: C4' within residue: .R<T 13>
> Created a new atom named: C5' within residue: .R<T 13>
> Created a new atom named: O4' within residue: .R<T 13>
> Created a new atom named: O4 within residue: .R<T 13>
> Created a new atom named: C4 within residue: .R<T 13>
> Created a new atom named: N3 within residue: .R<T 13>
> Created a new atom named: H3 within residue: .R<T 13>
> Created a new atom named: C2 within residue: .R<T 13>
> Created a new atom named: O2 within residue: .R<T 13>
> Created a new atom named: N1 within residue: .R<T 13>
> Created a new atom named: C6 within residue: .R<T 13>
> Created a new atom named: C5 within residue: .R<T 13>
> Created a new atom named: C7 within residue: .R<T 13>
> Creating new UNIT for residue: T sequence: 14
> Created a new atom named: P within residue: .R<T 14>
> Created a new atom named: O1P within residue: .R<T 14>
> Created a new atom named: O2P within residue: .R<T 14>
> Created a new atom named: O3' within residue: .R<T 14>
> Created a new atom named: O5' within residue: .R<T 14>
> Created a new atom named: C1' within residue: .R<T 14>
> Created a new atom named: C2' within residue: .R<T 14>
> Created a new atom named: C3' within residue: .R<T 14>
> Created a new atom named: C4' within residue: .R<T 14>
> Created a new atom named: C5' within residue: .R<T 14>
> Created a new atom named: O4' within residue: .R<T 14>
> Created a new atom named: O4 within residue: .R<T 14>
> Created a new atom named: C4 within residue: .R<T 14>
> Created a new atom named: N3 within residue: .R<T 14>
> Created a new atom named: H3 within residue: .R<T 14>
> Created a new atom named: C2 within residue: .R<T 14>
> Created a new atom named: O2 within residue: .R<T 14>
> Created a new atom named: N1 within residue: .R<T 14>
> Created a new atom named: C6 within residue: .R<T 14>
> Created a new atom named: C5 within residue: .R<T 14>
> Created a new atom named: C7 within residue: .R<T 14>
> Creating new UNIT for residue: T sequence: 15
> Created a new atom named: P within residue: .R<T 15>
> Created a new atom named: O1P within residue: .R<T 15>
> Created a new atom named: O2P within residue: .R<T 15>
> Created a new atom named: O3' within residue: .R<T 15>
> Created a new atom named: O5' within residue: .R<T 15>
> Created a new atom named: C1' within residue: .R<T 15>
> Created a new atom named: C2' within residue: .R<T 15>
> Created a new atom named: C3' within residue: .R<T 15>
> Created a new atom named: C4' within residue: .R<T 15>
> Created a new atom named: C5' within residue: .R<T 15>
> Created a new atom named: O4' within residue: .R<T 15>
> Created a new atom named: O4 within residue: .R<T 15>
> Created a new atom named: C4 within residue: .R<T 15>
> Created a new atom named: N3 within residue: .R<T 15>
> Created a new atom named: H3 within residue: .R<T 15>
> Created a new atom named: C2 within residue: .R<T 15>
> Created a new atom named: O2 within residue: .R<T 15>
> Created a new atom named: N1 within residue: .R<T 15>
> Created a new atom named: C6 within residue: .R<T 15>
> Created a new atom named: C5 within residue: .R<T 15>
> Created a new atom named: C7 within residue: .R<T 15>
> Creating new UNIT for residue: T sequence: 16
> Created a new atom named: P within residue: .R<T 16>
> Created a new atom named: O1P within residue: .R<T 16>
> Created a new atom named: O2P within residue: .R<T 16>
> Created a new atom named: O3' within residue: .R<T 16>
> Created a new atom named: O5' within residue: .R<T 16>
> Created a new atom named: C1' within residue: .R<T 16>
> Created a new atom named: C2' within residue: .R<T 16>
> Created a new atom named: C3' within residue: .R<T 16>
> Created a new atom named: C4' within residue: .R<T 16>
> Created a new atom named: C5' within residue: .R<T 16>
> Created a new atom named: O4' within residue: .R<T 16>
> Created a new atom named: O4 within residue: .R<T 16>
> Created a new atom named: C4 within residue: .R<T 16>
> Created a new atom named: N3 within residue: .R<T 16>
> Created a new atom named: H3 within residue: .R<T 16>
> Created a new atom named: C2 within residue: .R<T 16>
> Created a new atom named: O2 within residue: .R<T 16>
> Created a new atom named: N1 within residue: .R<T 16>
> Created a new atom named: C6 within residue: .R<T 16>
> Created a new atom named: C5 within residue: .R<T 16>
> Created a new atom named: C7 within residue: .R<T 16>
> Creating new UNIT for residue: T sequence: 17
> Created a new atom named: P within residue: .R<T 17>
> Created a new atom named: O1P within residue: .R<T 17>
> Created a new atom named: O2P within residue: .R<T 17>
> Created a new atom named: O3' within residue: .R<T 17>
> Created a new atom named: O5' within residue: .R<T 17>
> Created a new atom named: C1' within residue: .R<T 17>
> Created a new atom named: C2' within residue: .R<T 17>
> Created a new atom named: C3' within residue: .R<T 17>
> Created a new atom named: C4' within residue: .R<T 17>
> Created a new atom named: C5' within residue: .R<T 17>
> Created a new atom named: O4' within residue: .R<T 17>
> Created a new atom named: O4 within residue: .R<T 17>
> Created a new atom named: C4 within residue: .R<T 17>
> Created a new atom named: N3 within residue: .R<T 17>
> Created a new atom named: H3 within residue: .R<T 17>
> Created a new atom named: C2 within residue: .R<T 17>
> Created a new atom named: O2 within residue: .R<T 17>
> Created a new atom named: N1 within residue: .R<T 17>
> Created a new atom named: C6 within residue: .R<T 17>
> Created a new atom named: C5 within residue: .R<T 17>
> Created a new atom named: C7 within residue: .R<T 17>
> Creating new UNIT for residue: T sequence: 18
> Created a new atom named: P within residue: .R<T 18>
> Created a new atom named: O1P within residue: .R<T 18>
> Created a new atom named: O2P within residue: .R<T 18>
> Created a new atom named: O3' within residue: .R<T 18>
> Created a new atom named: O5' within residue: .R<T 18>
> Created a new atom named: C1' within residue: .R<T 18>
> Created a new atom named: C2' within residue: .R<T 18>
> Created a new atom named: C3' within residue: .R<T 18>
> Created a new atom named: C4' within residue: .R<T 18>
> Created a new atom named: C5' within residue: .R<T 18>
> Created a new atom named: O4' within residue: .R<T 18>
> Created a new atom named: O4 within residue: .R<T 18>
> Created a new atom named: C4 within residue: .R<T 18>
> Created a new atom named: N3 within residue: .R<T 18>
> Created a new atom named: H3 within residue: .R<T 18>
> Created a new atom named: C2 within residue: .R<T 18>
> Created a new atom named: O2 within residue: .R<T 18>
> Created a new atom named: N1 within residue: .R<T 18>
> Created a new atom named: C6 within residue: .R<T 18>
> Created a new atom named: C5 within residue: .R<T 18>
> Created a new atom named: C7 within residue: .R<T 18>
> Creating new UNIT for residue: T sequence: 19
> Created a new atom named: P within residue: .R<T 19>
> Created a new atom named: O1P within residue: .R<T 19>
> Created a new atom named: O2P within residue: .R<T 19>
> Created a new atom named: O3' within residue: .R<T 19>
> Created a new atom named: O5' within residue: .R<T 19>
> Created a new atom named: C1' within residue: .R<T 19>
> Created a new atom named: C2' within residue: .R<T 19>
> Created a new atom named: C3' within residue: .R<T 19>
> Created a new atom named: C4' within residue: .R<T 19>
> Created a new atom named: C5' within residue: .R<T 19>
> Created a new atom named: O4' within residue: .R<T 19>
> Created a new atom named: O4 within residue: .R<T 19>
> Created a new atom named: C4 within residue: .R<T 19>
> Created a new atom named: N3 within residue: .R<T 19>
> Created a new atom named: H3 within residue: .R<T 19>
> Created a new atom named: C2 within residue: .R<T 19>
> Created a new atom named: O2 within residue: .R<T 19>
> Created a new atom named: N1 within residue: .R<T 19>
> Created a new atom named: C6 within residue: .R<T 19>
> Created a new atom named: C5 within residue: .R<T 19>
> Created a new atom named: C7 within residue: .R<T 19>
> Creating new UNIT for residue: T3 sequence: 20
> Created a new atom named: P within residue: .R<T3 20>
> Created a new atom named: O1P within residue: .R<T3 20>
> Created a new atom named: O2P within residue: .R<T3 20>
> Created a new atom named: O3' within residue: .R<T3 20>
> Created a new atom named: O5' within residue: .R<T3 20>
> Created a new atom named: C1' within residue: .R<T3 20>
> Created a new atom named: C2' within residue: .R<T3 20>
> Created a new atom named: C3' within residue: .R<T3 20>
> Created a new atom named: C4' within residue: .R<T3 20>
> Created a new atom named: C5' within residue: .R<T3 20>
> Created a new atom named: O4' within residue: .R<T3 20>
> Created a new atom named: O4 within residue: .R<T3 20>
> Created a new atom named: C4 within residue: .R<T3 20>
> Created a new atom named: N3 within residue: .R<T3 20>
> Created a new atom named: H3 within residue: .R<T3 20>
> Created a new atom named: C2 within residue: .R<T3 20>
> Created a new atom named: O2 within residue: .R<T3 20>
> Created a new atom named: N1 within residue: .R<T3 20>
> Created a new atom named: C6 within residue: .R<T3 20>
> Created a new atom named: C5 within residue: .R<T3 20>
> Created a new atom named: C7 within residue: .R<T3 20>
> Created a new atom named: H3T within residue: .R<T3 20>
> total atoms in file: 438
> Leap added 80 missing atoms according to residue templates:
> 8 Heavy
> 72 H / lone pairs
> The file contained 254 atoms not in residue templates
>
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