AMBER: A few question about RDF input preparation

From: Maciej <makay22.wp.pl>
Date: Thu, 24 Mar 2005 12:13:10 +0100

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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Received on Thu Mar 24 2005 - 11:53:01 PST
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