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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Received on Thu Mar 24 2005 - 12:53:01 PST
