Tom I tried the addAtomTypes yesterday and today to no avail. Since I can build four ligands attached to the metal before the loadpdb command, I have proceeded to add and bond the remaining two ligands afterward. After the appropriate zMatrix command, I got the ligands right where I want them and LEaP spits out pdb, topology and coordinate files that I can use.
I think the chirality.c FATAL error that I was getting is a computer or compiler-specific thing.
John Cannon
Genetics Program Chair and
Associate Professor of
Molecular Microbiology and Immunology
University of Missouri
1 Hospital Drive
Columbia, Missouri 65212
-----Original Message-----
From: Tom Joseph [mailto:ttjoseph.gmail.com]
Sent: Monday, February 20, 2012 12:22 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Problem building octahedral coordinated ligands in LEaP
Ah, this is my mistake - I had forgotten to include the lines that inform leap of the hybridization types of these dummy atoms:
addAtomTypes {
{ "MM" "" "sp3" }
{ "DX" "" "sp3" }
{ "DY" "" "sp3" }
{ "DZ" "" "sp3" }
}
Using this leap command your example now works for me (after ensuring all the atom and type names are consistent).
Thanks for bringing this to my attention. I've updated the tarball on my site to reflect this.
--Tom
2012/2/20 Cannon, John F. <CannonJ.health.missouri.edu>
> 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
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Feb 20 2012 - 13:00:01 PST
