Thanks again for your help.
But when I do loadoff of the .lib file before loading the pdb, I get this:
> loadoff GLD.lib
Loading library: ./GLD.lib
> x = loadpdb goldcell.pdb
Loading 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 no idea why it's doing this. It does this no matter what I name the
atoms or residue, so I have no idea what template its going off of. Why
would it be doing this?
On another note, is it possible to run MD on atoms whose element is "?" in
xleap, and what is the purpose of the "unused" column in xleap? I'm asking
because I think I can get around these errors by just entering the
necessary info by hand rather than trying to create a template file, if it
comes to that...
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Received on Fri May 18 2018 - 15:30:02 PDT
