[AMBER] tleap error in reading structure generated from GLYCAM web

From: mish <smncbr.gmail.com>
Date: Fri, 24 Jun 2011 10:58:11 +0200

I am preparing a simulation of trisacharide. The PDB structure was built
using using GLYCAM web (*A-L-Fucp-(1-2)-[A-D-Galp-(1-3)]-B-D-Galp-(1-1)-OME*).
I wonder, when I read the same file in sander (using ff GLYCAM06), there is
an error :

ERROR: Comparing atoms
        .R<0fA 3>.A<C3 14>,
        .R<0fA 3>.A<C1 1>,
        .R<0fA 3>.A<H2 19>, and
        .R<0fA 3>.A<O2 20>
       to atoms
        .R<0fA 3>.A<C3 14>,
        .R<0LA 1>.A<C1 1>,
        .R<0fA 3>.A<H2 19>, and
        .R<0fA 3>.A<C1 1>
       This error may be due to faulty Connection atoms.
!FATAL ERROR----------------------------------------
!FATAL: In file [chirality.c], line 140
!FATAL: Message: Atom named C1 from 0LA did not match !

I really can not see any reason in the structure for such an error. Can any
of you point me please.

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Received on Fri Jun 24 2011 - 02:00:03 PDT
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