Dear Amber users and developers,
I am having a problem that I see in the archives was frequently asked but I see no solutions posted.
I am trying to build a protein model with LEaP that has manganese treated with a cationic dummy atom model (MN6).
I constantly get a fatal error like:
> pp1=loadpdb test.pdb
Loading PDB file: ./test.pdb
ERROR: Comparing atoms
.R<MN6 400>.A<DY2 4>,
.R<MN6 400>.A<DY1 3>,
.R<MN6 400>.A<DX2 2>, and
.R<MN6 400>.A<DX1 1>
to atoms
.R<MN6 400>.A<DY2 4>,
.R<MN6 400>.A<DY1 3>,
.R<MN6 400>.A<DZ1 5>, and
.R<MN6 400>.A<DX1 1>
This error may be due to faulty Connection atoms.
!FATAL ERROR----------------------------------------
!FATAL: In file [chirality.c], line 140
!FATAL: Message: Atom named DZ1 from MN6 did not match !
The test.pdb was trimmed down to just
HETATM 4722 MX MN6 400 82.265 50.290 15.843 2.0000 1.500 M
TER
END
I used Tom Joseph's MD6 and the cobalt hexamine parameters and the same thing happens. I am using Amber 10 and 11 on Linux.
When I build the MN6 using createAtom, createResidue, add, bond, createUnit, and zMatrix everything looks good until that loadpdb command.
In fact if I omit the last ligand, the error does not occur!
John Cannon
Genetics Program Chair and
Associate Professor of
Molecular Microbiology and Immunology
University of Missouri
1 Hospital Drive
Columbia, Missouri 65212
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Received on Mon Feb 20 2012 - 08:30:03 PST
