Thanks.
Yes, after few attempts I prepared the structure in same way as you have
mention in email. It workes . At that time I got confused that why it says
"Message: Atom named C1 from 0LA did not match !" but it was already present
in lib file.
Sincerely
mish
On Fri, Jun 24, 2011 at 4:09 PM, Lachele Foley (Lists) <lf.list.gmail.com>wrote:
> 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 <smncbr.gmail.com> 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
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Jun 24 2011 - 07:30:04 PDT
