Hi,
I tried to use tleap to create prmtop and inpcrd files and i got lot of
errors while doing that.
I am giving the complete details of this process
i typed
>tleap
>source leaprc.ff94
>1aj6=loadpdb 1AJ6.pdb
Loading PDB file: ./1AJ6.pdb
Splitting pdb file residue 1 into NOV and HOH
1 residues had naming problems.
Residues split, so res numbers will not correspond to pdb.
Unknown residue: NOV number: 194 type: Terminal/beginning
...relaxing end constraints to try for a dbase match
-no luck
Added missing heavy atom: .R<LYS 14>.A<CG 8>
Added missing heavy atom: .R<LYS 14>.A<CD 11>
Added missing heavy atom: .R<LYS 14>.A<CE 14>
Added missing heavy atom: .R<LYS 14>.A<NZ 17>
Added missing heavy atom: .R<ASP 49>.A<CG 8>
Added missing heavy atom: .R<ASP 49>.A<OD1 9>
Added missing heavy atom: .R<ASP 49>.A<OD2 10>
Added missing heavy atom: .R<LYS 57>.A<CD 11>
Added missing heavy atom: .R<LYS 57>.A<CE 14>
Added missing heavy atom: .R<LYS 57>.A<NZ 17>
Added missing heavy atom: .R<LYS 98>.A<CG 8>
Added missing heavy atom: .R<LYS 98>.A<CD 11>
Added missing heavy atom: .R<LYS 98>.A<CE 14>
Added missing heavy atom: .R<LYS 98>.A<NZ 17>
Added missing heavy atom: .R<GLN 116>.A<CG 8>
Added missing heavy atom: .R<GLN 116>.A<CD 11>
Added missing heavy atom: .R<GLN 116>.A<OE1 12>
Added missing heavy atom: .R<GLN 116>.A<NE2 13>
Added missing heavy atom: .R<GLU 147>.A<CG 8>
Added missing heavy atom: .R<GLU 147>.A<CD 11>
Added missing heavy atom: .R<GLU 147>.A<OE1 12>
Added missing heavy atom: .R<GLU 147>.A<OE2 13>
Added missing heavy atom: .R<LYS 150>.A<CD 11>
Added missing heavy atom: .R<LYS 150>.A<CE 14>
Added missing heavy atom: .R<LYS 150>.A<NZ 17>
Added missing heavy atom: .R<GLU 169>.A<CD 11>
Added missing heavy atom: .R<GLU 169>.A<OE1 12>
Added missing heavy atom: .R<GLU 169>.A<OE2 13>
Added missing heavy atom: .R<LYS 196>.A<CD 11>
Added missing heavy atom: .R<LYS 196>.A<CE 14>
Added missing heavy atom: .R<LYS 196>.A<NZ 17>
Added missing heavy atom: .R<GLU 201>.A<CD 11>
Added missing heavy atom: .R<GLU 201>.A<OE1 12>
Added missing heavy atom: .R<GLU 201>.A<OE2 13>
Added missing heavy atom: .R<CHIE 205>.A<OXT 18>
Creating new UNIT for residue: NOV sequence: 206
Created a new atom named: C1 within residue: .R<NOV 206>
Created a new atom named: O1 within residue: .R<NOV 206>
Created a new atom named: N1 within residue: .R<NOV 206>
Created a new atom named: C12 within residue: .R<NOV 206>
Created a new atom named: O4 within residue: .R<NOV 206>
Created a new atom named: O5 within residue: .R<NOV 206>
Created a new atom named: C27 within residue: .R<NOV 206>
Created a new atom named: C28 within residue: .R<NOV 206>
Created a new atom named: C29 within residue: .R<NOV 206>
Created a new atom named: O6 within residue: .R<NOV 206>
Created a new atom named: C30 within residue: .R<NOV 206>
Created a new atom named: O7 within residue: .R<NOV 206>
Created a new atom named: C31 within residue: .R<NOV 206>
Created a new atom named: C23 within residue: .R<NOV 206>
Created a new atom named: C26 within residue: .R<NOV 206>
Created a new atom named: O8 within residue: .R<NOV 206>
Created a new atom named: C3 within residue: .R<NOV 206>
Created a new atom named: C4 within residue: .R<NOV 206>
Created a new atom named: C2 within residue: .R<NOV 206>
Created a new atom named: C5 within residue: .R<NOV 206>
Created a new atom named: C9 within residue: .R<NOV 206>
Created a new atom named: C10 within residue: .R<NOV 206>
Created a new atom named: C11 within residue: .R<NOV 206>
Created a new atom named: O10 within residue: .R<NOV 206>
Created a new atom named: C6 within residue: .R<NOV 206>
Created a new atom named: O11 within residue: .R<NOV 206>
Created a new atom named: C7 within residue: .R<NOV 206>
Created a new atom named: C8 within residue: .R<NOV 206>
Created a new atom named: O9 within residue: .R<NOV 206>
Created a new atom named: N2 within residue: .R<NOV 206>
Created a new atom named: C13 within residue: .R<NOV 206>
Created a new atom named: O2 within residue: .R<NOV 206>
Created a new atom named: C14 within residue: .R<NOV 206>
Created a new atom named: C15 within residue: .R<NOV 206>
Created a new atom named: C16 within residue: .R<NOV 206>
Created a new atom named: C17 within residue: .R<NOV 206>
Created a new atom named: O3 within residue: .R<NOV 206>
Created a new atom named: C18 within residue: .R<NOV 206>
Created a new atom named: C19 within residue: .R<NOV 206>
Created a new atom named: C20 within residue: .R<NOV 206>
Created a new atom named: C21 within residue: .R<NOV 206>
Created a new atom named: C22 within residue: .R<NOV 206>
Created a new atom named: C24 within residue: .R<NOV 206>
Created a new atom named: C25 within residue: .R<NOV 206>
total atoms in file: 1592
Leap added 1701 missing atoms according to residue templates:
35 Heavy
1666 H / lone pairs
The file contained 44 atoms not in residue templates
> saveamberparm 1aj6 1aj6.prmtop 1aj6.inpcrd
Checking Unit.
WARNING: There is a bond of 6.015868 angstroms between:
------- .R<ILE 82>.A<C 18> and .R<VAL 83>.A<N 1>
WARNING: There is a bond of 15.902818 angstroms between:
------- .R<PHE 99>.A<C 19> and .R<SER 100>.A<N 1>
WARNING: The unperturbed charge of the unit: -7.000000 is not zero.
FATAL: Atom .R<NOV 206>.A<C1 1> does not have a type.
FATAL: Atom .R<NOV 206>.A<O1 2> does not have a type.
FATAL: Atom .R<NOV 206>.A<N1 3> does not have a type.
FATAL: Atom .R<NOV 206>.A<C12 4> does not have a type.
FATAL: Atom .R<NOV 206>.A<O4 5> does not have a type.
FATAL: Atom .R<NOV 206>.A<O5 6> does not have a type.
FATAL: Atom .R<NOV 206>.A<C27 7> does not have a type.
FATAL: Atom .R<NOV 206>.A<C28 8> does not have a type.
FATAL: Atom .R<NOV 206>.A<C29 9> does not have a type.
FATAL: Atom .R<NOV 206>.A<O6 10> does not have a type.
FATAL: Atom .R<NOV 206>.A<C30 11> does not have a type.
FATAL: Atom .R<NOV 206>.A<O7 12> does not have a type.
FATAL: Atom .R<NOV 206>.A<C31 13> does not have a type.
FATAL: Atom .R<NOV 206>.A<C23 14> does not have a type.
FATAL: Atom .R<NOV 206>.A<C26 15> does not have a type.
FATAL: Atom .R<NOV 206>.A<O8 16> does not have a type.
FATAL: Atom .R<NOV 206>.A<C3 17> does not have a type.
FATAL: Atom .R<NOV 206>.A<C4 18> does not have a type.
FATAL: Atom .R<NOV 206>.A<C2 19> does not have a type.
FATAL: Atom .R<NOV 206>.A<C5 20> does not have a type.
FATAL: Atom .R<NOV 206>.A<C9 21> does not have a type.
FATAL: Atom .R<NOV 206>.A<C10 22> does not have a type.
FATAL: Atom .R<NOV 206>.A<C11 23> does not have a type.
FATAL: Atom .R<NOV 206>.A<O10 24> does not have a type.
FATAL: Atom .R<NOV 206>.A<C6 25> does not have a type.
FATAL: Atom .R<NOV 206>.A<O11 26> does not have a type.
FATAL: Atom .R<NOV 206>.A<C7 27> does not have a type.
FATAL: Atom .R<NOV 206>.A<C8 28> does not have a type.
FATAL: Atom .R<NOV 206>.A<O9 29> does not have a type.
FATAL: Atom .R<NOV 206>.A<N2 30> does not have a type.
FATAL: Atom .R<NOV 206>.A<C13 31> does not have a type.
FATAL: Atom .R<NOV 206>.A<O2 32> does not have a type.
FATAL: Atom .R<NOV 206>.A<C14 33> does not have a type.
FATAL: Atom .R<NOV 206>.A<C15 34> does not have a type.
FATAL: Atom .R<NOV 206>.A<C16 35> does not have a type.
FATAL: Atom .R<NOV 206>.A<C17 36> does not have a type.
FATAL: Atom .R<NOV 206>.A<O3 37> does not have a type.
FATAL: Atom .R<NOV 206>.A<C18 38> does not have a type.
FATAL: Atom .R<NOV 206>.A<C19 39> does not have a type.
FATAL: Atom .R<NOV 206>.A<C20 40> does not have a type.
FATAL: Atom .R<NOV 206>.A<C21 41> does not have a type.
FATAL: Atom .R<NOV 206>.A<C22 42> does not have a type.
FATAL: Atom .R<NOV 206>.A<C24 43> does not have a type.
FATAL: Atom .R<NOV 206>.A<C25 44> does not have a type.
Failed to generate parameters
Parameter file was not saved.
These are the errors i am getting.
Can somebody please enlighten me on these errors?
I would also appreciate if you can give me some solutions.
P.S the pdb file 1AJ6 is the actual PDB id.
Thanks
Mike
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Received on Fri Mar 26 2004 - 07:53:00 PST
