AMBER Archive (2008)

Subject: Re: AMBER: Unable to create the top & crd files for a protein+ligand pdb structure

From: Jiten (jiten_at_postech.ac.kr)
Date: Sat Jan 12 2008 - 02:21:01 CST

Hi,

How did you create the lib file after the gaussian calculations. RESP charges and force field parameters should be assigned properly either using Antechamber or RED program. Did you check for the missing parameters using parmchk command in Antechamber?

Anyways, the error files shows that you have not loaded the MOL.lib files properly. You ligand molecule in PDB should have the same name as you created. Try the following steps.

1. Separate the ligand coordinate PDB
2. Load the lib/prep file and frcmod.MOL file you have created recently.
3. MOL = loadpdb your-ligand.pdb
4. Saveamberparm MOL MOL.top MOL.crd

If it works - that's good. Otherwise you need to fix it.

As for the proteins, it seems that your protien have some missing atoms in the PDB file or while you are processing some visualization tools it might have assign a wrong atom name to those amino acid residues. Look around if you protein is really missing those atoms as listed in the error.

Let us know if you still have a problem.

Best wishes,

Jiten

  ----- Original Message -----
  From: abiram abiram
  To: amber_at_scripps.edu
  Sent: Saturday, January 12, 2008 4:54 PM
  Subject: AMBER: Unable to create the top & crd files for a protein+ligand pdb structure

  Dear Amber Users,

      I am jus the beginner to amber. I was trying to create top and crd files for a pdb structure, which has a ligand bound to protein. Firstly, I have optimized the ligand in Gaussian and created the lib file for it following the protein+ligand tutorial in amber.

       While I was trying to load the whole pdb I could see that ligand molecule been added but it is not in the residue template..further I have tried creating the top and crd files, which ended with some error messages..below I have pasted the messages appeared while following the steps mentioned above..I have searched for answers in mailing lists..but I could not find..Kindly help me with to rectify the error..

> rec=loadpdb receptormod.pdb
  Loading PDB file: ./receptormod.pdb
    Added missing heavy atom: .R<NLYS 16>.A<CB 7>
    Added missing heavy atom: .R<NLYS 16>.A<CG 10>
    Added missing heavy atom: .R<NLYS 16>.A<CD 13>
    Added missing heavy atom: .R<NLYS 16>.A<CE 16>
    Added missing heavy atom: .R<NLYS 16>.A<NZ 19>
    Added missing heavy atom: .R<LYS 33>.A<CB 5>
    Added missing heavy atom: .R<LYS 33>.A<CG 8>
    Added missing heavy atom: .R<LYS 33>.A<CD 11>
    Added missing heavy atom: .R<LYS 33>.A<CE 14>
    Added missing heavy atom: .R<LYS 33>.A<NZ 17>
    Added missing heavy atom: .R<GLU 36>.A<CB 5>
    Added missing heavy atom: .R<GLU 36>.A<CG 8>
    Added missing heavy atom: .R<GLU 36>.A<CD 11>
    Added missing heavy atom: .R<GLU 36>.A<OE1 12>
    Added missing heavy atom: .R<GLU 36>.A<OE2 13>
    Added missing heavy atom: .R<LYS 54>.A<CB 5>
    Added missing heavy atom: .R<LYS 54>.A<CG 8>
    Added missing heavy atom: .R<LYS 54>.A<CD 11>
    Added missing heavy atom: .R<LYS 54>.A<CE 14>
    Added missing heavy atom: .R<LYS 54>.A<NZ 17>
    Added missing heavy atom: .R<ASP 76>.A<CB 5>
    Added missing heavy atom: .R<ASP 76>.A<CG 8>
    Added missing heavy atom: .R<ASP 76>.A<OD1 9>
    Added missing heavy atom: .R<ASP 76>.A<OD2 10>
    Added missing heavy atom: .R<LEU 103>.A<CB 5>
    Added missing heavy atom: .R<LEU 103>.A<CG 8>
    Added missing heavy atom: .R<LEU 103>.A<CD1 10>
    Added missing heavy atom: .R<LEU 103>.A<CD2 14>
    Added missing heavy atom: .R<LYS 113>.A<CG 8>
    Added missing heavy atom: .R<LYS 113>.A<CD 11>
    Added missing heavy atom: .R<LYS 113>.A<CE 14>
    Added missing heavy atom: .R<LYS 113>.A<NZ 17>
    Added missing heavy atom: .R<SER 127>.A<CB 5>
    Added missing heavy atom: .R<SER 127>.A<OG 8>
    Added missing heavy atom: .R<GLU 129>.A<CB 5>
    Added missing heavy atom: .R<GLU 129>.A<CG 8>
    Added missing heavy atom: .R<GLU 129>.A<CD 11>
    Added missing heavy atom: .R<GLU 129>.A<OE1 12>
    Added missing heavy atom: .R<GLU 129>.A<OE2 13>
    Added missing heavy atom: .R<LYS 133>.A<CB 5>
    Added missing heavy atom: .R<LYS 133>.A<CG 8>
    Added missing heavy atom: .R<LYS 133>.A<CD 11>
    Added missing heavy atom: .R<LYS 133>.A<CE 14>
    Added missing heavy atom: .R<LYS 133>.A<NZ 17>
    Added missing heavy atom: .R<GLN 134>.A<CB 5>
    Added missing heavy atom: .R<GLN 134>.A<CG 8>
    Added missing heavy atom: .R<GLN 134>.A<CD 11>
    Added missing heavy atom: .R<GLN 134>.A<OE1 12>
    Added missing heavy atom: .R<GLN 134>.A<NE2 13>
    Added missing heavy atom: .R<THR 135>.A<CB 5>
    Added missing heavy atom: .R<THR 135>.A<CG2 7>
    Added missing heavy atom: .R<THR 135>.A<OG1 11>
    Added missing heavy atom: .R<ARG 153>.A<CB 5>
    Added missing heavy atom: .R<ARG 153>.A<CG 8>
    Added missing heavy atom: .R<ARG 153>.A<CD 11>
    Added missing heavy atom: .R<ARG 153>.A<NE 14>
    Added missing heavy atom: .R<ARG 153>.A<CZ 16>
    Added missing heavy atom: .R<ARG 153>.A<NH1 17>
    Added missing heavy atom: .R<ARG 153>.A<NH2 20>
    Added missing heavy atom: .R<LYS 155>.A<CB 5>
    Added missing heavy atom: .R<LYS 155>.A<CG 8>
    Added missing heavy atom: .R<LYS 155>.A<CD 11>
    Added missing heavy atom: .R<LYS 155>.A<CE 14>
    Added missing heavy atom: .R<LYS 155>.A<NZ 17>
    Added missing heavy atom: .R<GLU 170>.A<CB 5>
    Added missing heavy atom: .R<GLU 170>.A<CG 8>
    Added missing heavy atom: .R<GLU 170>.A<CD 11>
    Added missing heavy atom: .R<GLU 170>.A<OE1 12>
    Added missing heavy atom: .R<GLU 170>.A<OE2 13>
    Added missing heavy atom: .R<LYS 187>.A<CB 5>
    Added missing heavy atom: .R<LYS 187>.A<CG 8>
    Added missing heavy atom: .R<LYS 187>.A<CD 11>
    Added missing heavy atom: .R<LYS 187>.A<CE 14>
    Added missing heavy atom: .R<LYS 187>.A<NZ 17>
    Added missing heavy atom: .R<LYS 189>.A<CB 5>
    Added missing heavy atom: .R<LYS 189>.A<CG 8>
    Added missing heavy atom: .R<LYS 189>.A<CD 11>
    Added missing heavy atom: .R<LYS 189>.A<CE 14>
    Added missing heavy atom: .R<LYS 189>.A<NZ 17>
    Added missing heavy atom: .R<SER 233>.A<CB 5>
    Added missing heavy atom: .R<SER 233>.A<OG 8>
    Added missing heavy atom: .R<CGLU 264>.A<OXT 16>
  Created a new atom named: N within residue: .R<MOL 265>
  Created a new atom named: CD within residue: .R<MOL 265>
  Created a new atom named: CD1 within residue: .R<MOL 265>
  Created a new atom named: CD2 within residue: .R<MOL 265>
  Created a new atom named: CA within residue: .R<MOL 265>
  Created a new atom named: CB within residue: .R<MOL 265>
  Created a new atom named: CB1 within residue: .R<MOL 265>
  Created a new atom named: CG within residue: .R<MOL 265>
  Created a new atom named: CG1 within residue: .R<MOL 265>
  Created a new atom named: CG2 within residue: .R<MOL 265>
  Created a new atom named: C within residue: .R<MOL 265>
  Created a new atom named: O within residue: .R<MOL 265>
  Created a new atom named: OD1 within residue: .R<MOL 265>
  Created a new atom named: OD2 within residue: .R<MOL 265>
  Created a new atom named: OXT within residue: .R<MOL 265>
    Added missing heavy atom: .R<MOL 265>.A<O2 10>
    Added missing heavy atom: .R<MOL 265>.A<C7 9>
    Added missing heavy atom: .R<MOL 265>.A<C6 8>
    Added missing heavy atom: .R<MOL 265>.A<O3 14>
    Added missing heavy atom: .R<MOL 265>.A<C3 4>
    Added missing heavy atom: .R<MOL 265>.A<C2 3>
    Added missing heavy atom: .R<MOL 265>.A<C4 5>
    Added missing heavy atom: .R<MOL 265>.A<N1 2>
    Added missing heavy atom: .R<MOL 265>.A<C5 6>
    Added missing heavy atom: .R<MOL 265>.A<C1 1>
    Added missing heavy atom: .R<MOL 265>.A<C8 11>
    Added missing heavy atom: .R<MOL 265>.A<O1 7>
    Added missing heavy atom: .R<MOL 265>.A<O4 15>
    Added missing heavy atom: .R<MOL 265>.A<C9 12>
    Added missing heavy atom: .R<MOL 265>.A<C10 13>
    total atoms in file: 1884
    Leap added 2101 missing atoms according to residue templates:
         97 Heavy
         2004 H / lone pairs
    The file contained 15 atoms not in residue templates

> saveamberparm rec pro.top pro.crd
  Checking Unit.
  WARNING: There is a bond of 8.578926 angstroms between:
  ------- .R<LYS 33>.A<C 21> and .R<MET 34>.A<N 1>
  WARNING: There is a bond of 12.710471 angstroms between:
  ------- .R<LYS 125>.A<C 21> and .R<GLU 126>.A<N 1>
  WARNING: The unperturbed charge of the unit: 5.000200 is not zero.
  FATAL: Atom .R<MOL 265>.A<N 30> does not have a type.
  FATAL: Atom .R<MOL 265>.A<CD 31> does not have a type.
  FATAL: Atom .R<MOL 265>.A<CD1 32> does not have a type.
  FATAL: Atom .R<MOL 265>.A<CD2 33> does not have a type.
  FATAL: Atom .R<MOL 265>.A<CA 34> does not have a type.
  FATAL: Atom .R<MOL 265>.A<CB 35> does not have a type.
  FATAL: Atom .R<MOL 265>.A<CB1 36> does not have a type.
  FATAL: Atom .R<MOL 265>.A<CG 37> does not have a type.
  FATAL: Atom .R<MOL 265>.A<CG1 38> does not have a type.
  FATAL: Atom .R<MOL 265>.A<CG2 39> does not have a type.
  FATAL: Atom .R<MOL 265>.A<C 40> does not have a type.
  FATAL: Atom .R<MOL 265>.A<O 41> does not have a type.
  FATAL: Atom .R<MOL 265>.A<OD1 42> does not have a type.
  FATAL: Atom .R<MOL 265>.A<OD2 43> does not have a type.
  FATAL: Atom .R<MOL 265>.A<OXT 44> does not have a type.
  Failed to generate parameters
  Parameter file was not saved.

  Rgds,
  A. Abiram

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