Hi Fabrício,
On 15/06/2012, at 4:44 AM, Fabrício Bracht wrote:
> 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.
What atom type is expected for your zinc ions? Specifically, when you were creating new types in the MCPB input, what did you call those for zinc? (You may in fact have multiple zinc types.) And have you explicitly told LEaP what zinc types to create, or is it just guessing them? Do you have a leaprc file that you're using, and if so what do the sections that deal with zinc in any way, shape or form look like?
> 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?
No, that's not correct. Parameter entries provide general descriptions of what bonds should look like. Whether such a bond exists or not is considered part of the topology, and must be specified separately, for example via the "bond" command.
Hope that helps,
Ben
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Received on Thu Jun 14 2012 - 14:00:03 PDT
