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

From: Lachele Foley (Lists) <"Lachele>
Date: Fri, 24 Jun 2011 10:09:50 -0400

This sounds like a bonding issue. The structure you mention is
branched. Do you have TER cards at the appropriate locations in the
PDB file? You also need to include explicit bond commands in the
tleap input. If you think this might be the issue, download the
"Formatted PDB", it will contain TER cards in the right places. You
can also use the LINK cards in that file to guide generation of the
bond commands. Note that you only need bond commands for residues
separated by a TER card.

To check for bonding issues, or to make sure your TER cards and bond
commands are right, open the top and crd files in vmd (use Amber 7
Parm and Amber 7 Restart as the file types).

If none of what I said above helps, send me the pdb file and tell me
which commands you used in tleap.

:-) Lachele

On Fri, Jun 24, 2011 at 4:58 AM, mish <> wrote:
> Hi:
> 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.
> Sincerely
> mish
> _______________________________________________
> AMBER mailing list

:-) Lachele
Lachele Foley
Athens, GA USA
AMBER mailing list
Received on Fri Jun 24 2011 - 07:30:03 PDT
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