AMBER Archive (2004)

Subject: RE: AMBER: tleap error and warnings

From: Chris Moth (chris.moth_at_vanderbilt.edu)
Date: Fri Mar 26 2004 - 09:34:08 CST

Hi Mike:

Welcome to the world of molecular dynamics simulation setup :)

Novobiocin (NOV) is not built into the AMBER paramter file set. You must now
review the molecule, and assign atom types and electrostatic charges to make a
".prp" file. See the AMBER manual for details. And, there will be other
helpful hints on the reflector.

As for the addition of heavy atoms for side chains.... Let's look at one
example. In the .pdb, Lys14 is not fully resolved - so the crystallographers
only gave coordinates for part of the residue:

ATOM 16 N LYS 14 71.101 11.339 25.827 1.00 40.48 N
 
ATOM 17 CA LYS 14 70.322 12.472 25.373 1.00 40.85 C
 
ATOM 18 C LYS 14 68.917 12.314 25.890 1.00 43.35 C
 
ATOM 19 O LYS 14 68.340 13.275 26.423 1.00 41.81 O
 
ATOM 20 CB LYS 14 70.329 12.534 23.856 1.00 41.87 C

The AMBER warnings are telling you that tleap is filling in the rest of
the residue:

> 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>

tleap is also adding protons where needed - without any warnings.

You need to be comfortable with how this gets done - use ambpdb to review
the structure after you save prmtop and coordainte files.

It sounds like you are just getting your feet wet with MD - so you might
consider removing the NOV molecule and seeing if you can get a simulation
going without it first. Careful paramterization of NOV will be your biggest
job.

>===== Original Message From "Mike" <amber_list_at_speedpost.net> =====
>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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Chris Moth
chris.moth_at_vanderbilt.edu

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