AMBER Archive (2005)

Subject: Re: AMBER: A few question about RDF input preparation

From: Wei Zhang (zweig_at_pku.edu.cn)
Date: Thu Mar 24 2005 - 05:58:47 CST


Dear Maciej,

If you are using AMBER 8.0, you can use antechamber to parametrize your molecule.

 Wei Zhang
  ----- Original Message -----
  From: Maciej
  To: amber
  Sent: Thursday, March 24, 2005 7:13 PM
  Subject: AMBER: A few question about RDF input preparation

  This is this what jumps out after I turn on leap to recording prefiles for 8 - oxodg:

> OXO=loadpdb oxo.pdb

  Loading PDB file: ./oxo.pdb

  Created a new atom named: OH8 within residue: .R<DG3 1>

  Created a new atom named: H within residue: .R<DG3 1>

    total atoms in file: 34

    Leap added 2 missing atoms according to residue templates:

         2 H / lone pairs

    The file contained 2 atoms not in residue templates

    Since added/missing = extra, there is a high probability

    of atoms with 'incorrect' names; you may want to

    use addPdbAtomMap to map these names, or change in file

   

  When i change OH8 to O8 or O i have that msg:

   

  OXO=loadpdb oxo.pdb

  Loading PDB file: ./oxo.pdb

    Added missing heavy atom: .R<DG3 1>.A<C3' 28>

    Added missing heavy atom: .R<DG3 1>.A<C2' 30>

    Added missing heavy atom: .R<DG3 1>.A<O3' 33>

    Added missing heavy atom: .R<DG3 1>.A<C4 27>

    Added missing heavy atom: .R<DG3 1>.A<C5 17>

    Added missing heavy atom: .R<DG3 1>.A<N3 26>

    Added missing heavy atom: .R<DG3 1>.A<N7 16>

    Added missing heavy atom: .R<DG3 1>.A<C6 18>

    Added missing heavy atom: .R<DG3 1>.A<C2 22>

    Added missing heavy atom: .R<DG3 1>.A<O6 19>

    Added missing heavy atom: .R<DG3 1>.A<N1 20>

    Added missing heavy atom: .R<DG3 1>.A<N2 23>

  Creating new UNIT for residue: sequence: 2

  Created a new atom named: O within residue: .R< 0>

  Creating new UNIT for residue: sequence: 3

  Created a new atom named: N7 within residue: .R< 0>

  Created a new atom named: C5 within residue: .R< 0>

  Created a new atom named: C6 within residue: .R< 0>

  Created a new atom named: O6 within residue: .R< 0>

  Created a new atom named: N1 within residue: .R< 0>

  Created a new atom named: H1 within residue: .R< 0>

  Created a new atom named: C2 within residue: .R< 0>

  Created a new atom named: N2 within residue: .R< 0>

  Created a new atom named: H21 within residue: .R< 0>

  Created a new atom named: H22 within residue: .R< 0>

  Created a new atom named: N3 within residue: .R< 0>

  Created a new atom named: C4 within residue: .R< 0>

  Created a new atom named: C3* within residue: .R< 0>

  Created a new atom named: H3* within residue: .R< 0>

  Created a new atom named: C2* within residue: .R< 0>

  Created a new atom named: H2*1 within residue: .R< 0>

  Created a new atom named: H2*2 within residue: .R< 0>

  Created a new atom named: O3* within residue: .R< 0>

  Created a new atom named: H within residue: .R< 0>

    total atoms in file: 34

    Leap added 20 missing atoms according to residue templates:

         12 Heavy

         8 H / lone pairs

    The file contained 20 atoms not in residue templates

    Since added/missing = extra, there is a high probability

    of atoms with 'incorrect' names; you may want to

    use addPdbAtomMap to map these names, or change in file

   

  How should i parametrize this molecule ?

  How to make file for ptraj to count RDF betweenoxygen atoms I water box ?

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