AMBER Archive (2005)

Subject: AMBER: leap question

From: Kara Di Giorgio (kdigiorgio_at_sbcglobal.net)
Date: Fri Aug 05 2005 - 11:38:47 CDT

I'm trying to combine my units in leap into a single molecule to make
prmtop in inpcrd files. I created a molecule and have it correctly
formatted in xLeap. (It was made out of a crown-ether like organic
portion and a Ni atom that were merged. I called the new unit NCH.) I
want to put the NCH into a piece of DNA as an intercalator in place of
an existing molecule. I changed the atom/residue names of the chosen
overlap atoms in the intercalator-DNA pdb file to those of the matching
atoms in NCR and deleted all of the other old intercalator atoms. I
load NCH into leap, get that settled correctly and then try and load
the DNA pdb file, hoping that leap will recognize the atoms and place
NCH in the correct place. (I've used this method in the past and it
has been fine. This time, it doesn't recognize the atoms, places the
NCH a ways away and mashes it up. I get the following error in
leap.log:

> NiCR2H = loadpdb NiCR2H_dna_mod.pdb
Loading PDB file: ./NiCR2H_dna_mod.pdb
Matching PDB residue names to LEaP variables.
Mapped residue C5, term: Terminal/beginning, seq. number: 0 to: DC5.
Mapped residue G, term: Nonterminal, seq. number: 1 to: DG.
Mapped residue C, term: Nonterminal, seq. number: 2 to: DC.
Mapped residue G, term: Nonterminal, seq. number: 3 to: DG.
Mapped residue C, term: Nonterminal, seq. number: 4 to: DC.
Mapped residue G3, term: Terminal/last, seq. number: 5 to: DG3.
Mapped residue C5, term: Terminal/beginning, seq. number: 6 to: DC5.
Mapped residue G, term: Nonterminal, seq. number: 7 to: DG.
Mapped residue C, term: Nonterminal, seq. number: 8 to: DC.
Mapped residue G, term: Nonterminal, seq. number: 9 to: DG.
Mapped residue C, term: Nonterminal, seq. number: 10 to: DC.
Mapped residue G3, term: Terminal/last, seq. number: 11 to: DG3.
(Residue 12: NCH, Terminal/last, was not found in name map.)
Joining DC5 - DG
Joining DG - DC
Joining DC - DG
Joining DG - DC
Joining DC - DG3
Joining DC5 - DG
Joining DG - DC
Joining DC - DG
Joining DG - DC
Joining DC - DG3
Created a new atom named: C4 within residue: .R<Ni 13>
Created a new atom named: C6 within residue: .R<Ni 13>
   Added missing heavy atom: .R<Ni 13>.A<Ni 1>
   Added missing heavy atom: .R<NCH 14>.A<N1 8>
   Added missing heavy atom: .R<NCH 14>.A<N2 15>
   Added missing heavy atom: .R<NCH 14>.A<N3 25>
   Added missing heavy atom: .R<NCH 14>.A<N 36>
   Added missing heavy atom: .R<NCH 14>.A<C7 9>
   Added missing heavy atom: .R<NCH 14>.A<C3 7>
   Added missing heavy atom: .R<NCH 14>.A<C9 16>
   Added missing heavy atom: .R<NCH 14>.A<C8 10>
   Added missing heavy atom: .R<NCH 14>.A<C14 27>
   Added missing heavy atom: .R<NCH 14>.A<C11 22>
   Added missing heavy atom: .R<NCH 14>.A<C2 37>
   Added missing heavy atom: .R<NCH 14>.A<C1 33>
   Added missing heavy atom: .R<NCH 14>.A<C6 1>
   Added missing heavy atom: .R<NCH 14>.A<C4 5>
   Added missing heavy atom: .R<NCH 14>.A<C10 19>
   Added missing heavy atom: .R<NCH 14>.A<C13 11>
   Added missing heavy atom: .R<NCH 14>.A<C 30>
   Added missing heavy atom: .R<NCH 14>.A<C12 38>
   Added missing heavy atom: .R<NCH 14>.A<C5 3>
   total atoms in file: 266
   Leap added 154 missing atoms according to residue templates:
        20 Heavy
        134 H / lone pairs
   The file contained 2 atoms not in residue templates

It looks like it's not thinking that NCH is a single unit, maybe? I'm
not sure what's going on.

Thanks,

Kara Di Giorgio

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