AMBER Archive (2008)

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

From: abiram abiram (mail2abiram_at_yahoo.co.in)
Date: Sat Jan 12 2008 - 01:54:01 CST

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

       
---------------------------------
 Did you know? You can CHAT without downloading messenger. Click here
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu