Thank you for the reply.
But I want to keep the coordinates as in the original pdb file, and I do
notice that the ordering of atoms in my pdb file are different from GLYCAM
convention.
So could anyone suggest a way to format my oligosaccharide in accordance
with GLYCAM06 while retaining the coordinates (structure) of my original pdb
file?
Thanks,
Yun
On Fri, Aug 12, 2011 at 10:00 AM, Oliver Grant <olivercgrant.gmail.com>wrote:
> Hi,
>
> Not sure what the problem is without looking at your pdb input file. I
> suggest going to glycamweb and building your oligosaccharide and comparing
> that to what you have.
>
> Oliver
>
> On 12 August 2011 04:42, Yun Shi <yunshi09.gmail.com> wrote:
>
> > Hi All,
> >
> > Sorry for this lower-level question, but I searched the archive and still
> > did not solve it.
> >
> > So I was trying to load a pdb file (only one oligosaccharide molecule)
> > after
> > source leaprc.GLYCAM_06, but what I got was
> >
> > ERROR: Comparing atoms
> > .R<0hA 1>.A<C3 14>,
> > .R<0hA 1>.A<C1 1>,
> > .R<0hA 1>.A<H2 19>, and
> > .R<0hA 1>.A<O2 20>
> > to atoms
> > .R<0hA 1>.A<C3 14>,
> > .R<2hA 1>.A<C1 1>,
> > .R<0hA 1>.A<H2 19>, and
> > .R<0hA 1>.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 2hA did not match !
> > !
> > !ABORTING.
> >
> > So what it really means by "faulty Connection atoms"? I have already
> > changed
> > the sugar names according to GLYCAM naming convention.
> >
> > Any help is appreciated!
> >
> > Yun
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Aug 12 2011 - 10:30:04 PDT
