I have finally finished calculating the parameters for my ZN active
site. I used the same procedure described in MTK++ manual.
Successfully generated the prep and frcmod files. Loaded the protein
structure into tleap in addition to loading leaprc.ff12SB forcefield
files. When I type "check myprotein", leap tells me that, apart from a
few close contact warnings (no big deal, I've checked), the structure
is ok. When I try saving the prmtop and the inpcrd files, suddenly
leap tells me that:
For atom: .R<ZN1 339>.A<ZN 1> Could not find type: ZN
For atom: .R<ZN1 341>.A<ZN 1> Could not find type: ZN
, and it does not save the files.
Some help here would be great.
One other question is. The bond parameters are described in the frcmod
file I created using MCPB, right? So, I'm supposing that there is no
necessity in specifying the bonds again in leap by using the command
"bond", right? What I mean is that, leap has already recognized that
the active site residues and my ZN atom are already linked, correct?
Thank you
Fabrício Bracht
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Received on Thu Jun 14 2012 - 10:00:03 PDT
