On Fri, 2012-03-30 at 18:22 +0530, abinayar.imsc.res.in wrote:
> Dear amber users,
>
> I am getting the following error while running xleap in AMBER11
>
> FATAL: Atom .R<VAL 7>.A<G11 17> does not have a type.
> FATAL: Atom .R<VAL 7>.A<G12 18> does not have a type.
> FATAL: Atom .R<VAL 7>.A<G13 19> does not have a type.
> FATAL: Atom .R<VAL 7>.A<G21 20> does not have a type.
> FATAL: Atom .R<VAL 7>.A<G22 21> does not have a type.
> FATAL: Atom .R<VAL 7>.A<G23 22> does not have a type.
> FATAL: Atom .R<VAL 11>.A<G11 17> does not have a type.
> FATAL: Atom .R<VAL 11>.A<G12 18> does not have a type.
> FATAL: Atom .R<VAL 11>.A<G13 19> does not have a type.
> FATAL: Atom .R<VAL 11>.A<G21 20> does not have a type.
> FATAL: Atom .R<VAL 11>.A<G22 21> does not have a type.
Your atom names are very weird. Where did you get your PDB?
The atom names in the PDB must match the atom names in the template.
The standard amino acid templates (which include VALine), are found in
$AMBERHOME/dat/leap/lib/ -- look for allamino94.lib or something
similar.
Whatever program you used to get your PDB has mangled the names so that
leap doesn't recognize them in Valine anymore.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Mar 30 2012 - 07:30:06 PDT
