AMBER Archive (2007)

Subject: Re: AMBER: xLeap "Could not find type" error

From: David A. Case (case_at_scripps.edu)
Date: Tue Aug 21 2007 - 19:40:09 CDT

On Tue, Aug 21, 2007, Lili Peng wrote:
>
> I am trying to load a .MOL2 file in xleap, but when I try to save the prmtop
> and inpcrd files, I get the error messages:
>
> "For atom: .R<GLU2 6>.A<CA 2> Could not fine type: C.3
> For atom: .R<GLU2 6>.A<CB 3> Could not fine type: C.3
> For atom: .R<GLU2 6>.A<CG 4> Could not fine type: C.3
> For atom: .R<GLU2 6>.A<CD 5> Could not fine type: C.2
> For atom: .R<GLU2 6>.A<OE1 6> Could not fine type: O.2
> For atom: .R<GLU2 6>.A<C 7> Could not fine type: C.2
> ..."

These sounds like sybyl atom types (or something). They are neither Amber nor
gaff atom types. You molecule looks something like 6 or 7 glu residues all
merged together in a single residue. You probably want to convert this mol2
file to a pdb file that looks like 6 glu residues, then load that.

....good luck....dac

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