AMBER Archive (2007)

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

From: Lili Peng (lilipeng_at_gmail.com)
Date: Tue Aug 21 2007 - 20:17:44 CDT

Hi Dr. Case,

Thanks for your help. I did convert the MOL2 file into PDB format, however,
the bonds I manually added between the C and N atoms in glutamic acid side
chain residues were missing in the PDB file. I'd like to note that I'm
using Acclerys' Discovery Suite software to create my MOL2 (and PDB) files.

Do you have any suggestions how to go about this problem? My initial guess
is that I can use tleap to manually add the bonds between the C and N atoms
in the PDB file. Your thoughts would be appreciated.

Regards,
Lili

On 8/21/07, David A. Case <case_at_scripps.edu> wrote:
>
> 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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