Here are some more details:
As a test, I have a pdb called goldcell.pdb, containing 4 gold atoms with
atom name AU and residue name GLD. No bonds at all.
I thought that my .lib file would be ok for describing this structure (or
any amount of them that I need, as long as they have the same residue
name), in much the same way that one .lib file for Alanine is used as a
template for the dozens of residues named ALA in a protein, for example.
In Xleap I do:
*GLD = loadpdb goldcell.pdb *
*edit GLD *(here I enter AU for type and Au for element, save and quit. The
atom name is also AU in the pdb file...is it a problem that the name and
type are the same?)
*saveoff GLD GLD.lib*
I then placed GLD.lib in $AMBERHOME/dat/leap/lib with all the other .libs.
I thought that xleap will now read this .lib file and match any
subsequently loaded pdb file with residue name GLD to this .lib template.
Am I wrong about that?
After making GLD.lib I still get unknown residue errors:
*> x = loadpdb goldcell.pdbLoading PDB file: ./goldcell.pdbUnknown residue:
GLD number: 0 type: Terminal/beginning..relaxing end constraints to try
for a dbase match -no luckUnknown residue: GLD number: 1 type:
NonterminalUnknown residue: GLD number: 2 type: NonterminalUnknown
residue: GLD number: 3 type: Terminal/last..relaxing end constraints to
try for a dbase match -no luckCreating new UNIT for residue: GLD sequence:
1Created a new atom named: AU within residue: .R<GLD 1>Creating new UNIT
for residue: GLD sequence: 2Created a new atom named: AU within residue:
.R<GLD 2>Creating new UNIT for residue: GLD sequence: 3Created a new atom
named: AU within residue: .R<GLD 3>Creating new UNIT for residue: GLD
sequence: 4Created a new atom named: AU within residue: .R<GLD 4> total
atoms in file: 4 The file contained 4 atoms not in residue templates*
Even more weirdly, if I loadoff GLD.lib and then try to load goldcell.pdb
again, I get this:
*> loadoff GLD.libLoading library: ./GLD.lib> a = loadpdb
goldcell.pdbLoading PDB file: ./goldcell.pdb Added missing heavy atom:
.R<GLD 2>.A<AU 1> Added missing heavy atom: .R<GLD 3>.A<AU 1> Added
missing heavy atom: .R<GLD 4>.A<AU 1> Added missing heavy atom: .R<GLD
3>.A<AU 1> Added missing heavy atom: .R<GLD 4>.A<AU 1> Added missing
heavy atom: .R<GLD 5>.A<AU 1> Added missing heavy atom: .R<GLD 4>.A<AU 1>
Added missing heavy atom: .R<GLD 5>.A<AU 1> Added missing heavy atom:
.R<GLD 6>.A<AU 1> Added missing heavy atom: .R<GLD 5>.A<AU 1> Added
missing heavy atom: .R<GLD 6>.A<AU 1> Added missing heavy atom: .R<GLD
7>.A<AU 1> total atoms in file: 4 Leap added 12 missing atoms according
to residue templates: 12 Heavy*
I have used two different random residue names other than GLD to see if
that would help, but it changed nothing.
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Received on Thu May 17 2018 - 15:00:03 PDT
